• Korean Journal of Plant Resources
• /
• v.21 no.3
• /
• pp.210-215
• /
• 2008

Gene-expression analysis is increasingly important in biological research, with real-time reverse PCR (RTPCR) becoming the method of choice for high-throughput and accurate expression profiling of selected genes. However, this technique requires important preliminary work for standardizing and optimizing the many parameters involved in the analysis. Plant stress studies are more and more based on gene expression. The analysis of gene expression requires sensitive and reproducible measurements for specific mRNA sequence. Several genes are regulated in response to abitoic stresses, such as salinity, and their gene products function in stress response and tolerance. The design of the primers and TaqMan probes for real-time PCR assays were carried out using the Primer $Express^{TM}$ software 3.0. The PCR efficiency was estimated through the linear regression of the dilution curve. To understand the expression pattern of various genes under salt stressed condition, we have developed a unique public resource of 9 stress-related genes in poplar. In this study, real-time RT-PCR was used to quantify the transcript level of 10 genes (9 stress-related genes and 1 house keeping gene) that could play a role in adaptation of Populus davidiana. Real-time RT-PCR analyses exhibited different expression ratios of related genes. The data obtained showed that determination of mRNA levels could constitute a new approach to study the stress response of P. davidiana after adaptation during growth in salinity condition.

• Current Research on Agriculture and Life Sciences
• /
• v.32 no.1
• /
• pp.43-52
• /
• 2014

Reactive oxygen and nitrogen species (ROS and RNS, respectively) are messengers that carry signals to alter the redox state in order to activate plant responses and other physiological processes, such as differentiation, aging, senescence, and pathogen defense. Quite a large number of genes are involved in this signaling and lead to oxidative stress in plants. Although the role of ROS/RNS during stress conditions is well documented, a comprehensive list of genes and comparative study of these genes has not yet been completed. Accordingly, the in silico identification of oxidative stress-related genes was performed for soybeans and Arabidopsis. These genes were also studied in relation to multiple domain prediction. The presence of domains like dehydogenase and ATPase suggests that these genes are involved in various metabolic processes, as well as the transportation of ions under optimal environmental conditions. In addition to a sequence analysis, a phylogenetic analysis was also performed to identify orthologous pairs among the soybean and Arabidopsis oxidative stress-related genes based on neighbor joining. This study was also conducted with the objective of further understanding the complex molecular signaling mechanism in plants under various stress conditions.

• Journal of Plant Biotechnology
• /
• v.45 no.4
• /
• pp.306-314
• /
• 2018

Korean ginseng (Panax ginseng) has long been cultivated as an important economic medicinal plant. Owing to the seasonal and long-term agricultural cultivation methods of Korean ginseng, they are always vulnerable to various environmental stress conditions. ABSCISIC ACID (ABA) is an essential plant hormone associated with seed development and diverse abiotic stress responses including drought, cold and salinity stress. By modulating ABA responses, plants can regulate their immune responses and growth patterns to increase their ability to tolerate stress. With recent advances in genome sequencing technology, we first reported the functional features of genes related to canonical ABA signaling pathway in P. ginseng genome. Based on the protein sequences and functional genomic analysis of Arabidopsis thaliana, the ABA related genes were successfully identified. Our functional genomic characterizations clearly showed that the ABA signaling related genes consisting the ABA receptor proteins (PgPYLs), kinase family (PgSnRKs) and transcription factors (PgABFs, PgABI3s and PgABI5s) were evolutionary conserved in the P. ginseng genome. We confirmed that overexpressing ABA related genes of P. ginseng completely restored the ABA responses and stress tolerance in ABA defective Arabidopsis mutants. Finally, tissue and age specific spatio-temporal expression patterns of the identified ABA-related genes in P. ginseng tissues were also classified using various available RNA sequencing data. This study provides ABA signal transduction related genes and their functional genomic information related to the growth and development of Korean ginseng. Additionally, the results of this study could be useful in the breeding or artificial selection of ginseng which is resistant to various stresses.

• Journal of Plant Biotechnology
• /
• v.50
• /
• pp.225-231
• /
• 2023

Cold stress is one of the most vulnerable environmental stresses that affect plant growth and crop yields. With the recent advancements in genetic approaches using Arabidopsis and other model systems, genes involved in cold-stress response have been identified and the key cold signaling factors have been characterized. Exposure to low-temperature stress triggers the activation of a set of genes known as cold regulatory (COR) genes. This activation process plays a crucial role in enhancing the resistance of plants to cold and freezing stress. The inducer of the C-repeatbinding factor (CBF) expression 1-CBF module (ICE1-CBF module) is a key cold signaling pathway regulator that enhances the expression of downstream COR genes; however, this signaling module in Panax ginseng remains elusive. Here, we identified cold-signaling-related genes, PgCBF1, PgCBF3, and PgICE1 and conducted functional genomic analysis with a heterologous system. We confirmed that the overexpression of cold- PgCBF3 in the cbf1/2/3 triple Arabidopsis mutant compensated for the cold stress-induced deficiency of COR15A and salt-stress tolerance. In addition, nuclearlocalized PgICE1 has evolutionarily conserved phosphorylation sites that are modulated by brassinsteroid insensitive 2 (PgBIN2) and sucrose non-fermenting 1 (SNF1)-related protein kinase 3 (PgSnRK3), with which it physically interacted in a yeast two-hybrid assay. Overall, our data reveal that the regulators identified in our study, PgICE1 and PgCBFs, are evolutionarily conserved in the P. ginseng genome and are functionally involved in cold and abiotic stress responses.

• Journal of fish pathology
• /
• v.15 no.2
• /
• pp.83-92
• /
• 2002

EST analysis was performed to identify stress-responsive and immune-related genes from mud loach (Misgurnus mizolepis), cDNA libraries were constructed with liver, intestine and kidney tissues and randomly chosen clones (216 for liver, 198 for intestine and 224 for kidney) were subjected to automated sequence analysis. Of 638 clones sequenced in totlal, approximalely 25% of ESTs was novel sequences (no match to GenBank) or sequences with high homology to hypothrtical/unknown genes. Several potential stress-responsive biomarker and/or immure-related genes were identified in all the tissues examined. It included lectin, MHC class I/II proteins, proteinase inhibitors, superoxide dismulase, catalase, glutathionc-S. transferase, heat-shock protein, warm temperature acclimation protein, complements, methylrransferasc, zinc finger proteins, macrophage maturation associated protein, and others. This information will offer new possibilities as fundamental baseline data for the molecular genetics and breeding of this species with an emphasis on the development of stress. (and disease)-resistsnt fish.

• Development and Reproduction
• /
• v.24 no.1
• /
• pp.31-41
• /
• 2020

We investigated the effects of endoplasmic reticulum (ER) stress inhibitor and antioxidant treatments during the micromanipulation of somatic cell nuclear transfer (SCNT) on in vitro development of SCNT embryos. Tauroursodeoxycholic acid (TUDCA), an ER stress inhibitor and vitamin C (Vit. C), an antioxidant, were treated by alone or in combination, then, the level of X-box binding protein 1 (Xbp1) splicing and the expressions of ER stress-associated genes, oxidative stress-related genes, and apoptotic genes were confirmed in the 1-cell and blastocyst stages. In the 1-cell stage, the levels of Xbp1 splicing were significantly decreased in TUDCA and Vit. C treatment groups compared to the control (p<0.05). In addition, the expression levels of most ER stress-associated genes and oxidative stress-related genes were significantly lower in all treatment groups than the control (p<0.05), and the transcript levels of apoptotic genes were also significantly lower in all treatment groups than the control (p<0.05). In the blastocyst stage, decreased expression of ER stress-, oxidative stress-, and apoptosis-related genes were observed only in some treatments. However, the blastocyst formation rates in TUDCA and Vit. C treatment groups (24.8% and 22.0%, respectively) and mean blastocyst cell number in all treatment groups (59.7±4.3 to 63.5±3.3) were significantly higher (p<0.05) than those of control. The results showed that the TUDCA or Vit. C treatment during micromanipulation inhibited both ER and oxidative stresses in the early stage of SCNT embryos, thereby reducing cell damage and promoting in vitro development.

• Journal of Plant Biotechnology
• /
• v.37 no.4
• /
• pp.472-482
• /
• 2010

For the massive screening of the genes related to oxidative stress, a cDNA library was constructed from hot pepper (Capsicum annuum L. cv. Nockkwang) leaves treated with methyl viologen. From this library, 1,589 cDNA clones were sequenced from their 5' ends. The sequences were clustered into 1,252 unigenes comprised of 152 contigs and 1,100 singletons. Similarity search against NCBI protein database identified 1,005 ESTs (80.3%) as Known, 197 ESTs (15.7%) as Unknown, and 50 ESTs (3.99%) as No hit. In the ESTs, oxidative stress-related genes such as ascorbate peroxidase, catalase, and osmotin precursor were highly expressed. The cDNA microarray containing 1,252 unigenes was constructed and used to analyze their expression upon methyl viologen treatment. Analyses of the hybridization revealed that various stress-related genes such as peroxidase, tyrosine aminotransferase, and omega-6 fatty acid desaturase, were induced and some metabolism related genes such as aldolase and ketol-acid reductoisomerase, were repressed by methyl viologen treatment, respectively. The information from this study will be used for further study on the functional roles of oxidative stress-related genes and signaling network of oxidative stress in hot pepper.

• The Plant Pathology Journal
• /
• v.25 no.2
• /
• pp.172-178
• /
• 2009

To obtain global gene expression profiles of Arabidopsis thaliana by acid stress, seedlings were subjected to low pH stress. Using Affymetrix AH1 chips covering 24,000 genes, we analyzed gene expression patterns. Fifty-four genes were up-regulated, and 38 were down-regulated more than 3-fold after 2 h of acid stress (pH 3.0). Several defense and abiotic stress-related genes were recognized among the up-regulated genes and peroxidase and extensin genes were identified among the down-regulated genes. After 12 h treatment, relatively fewer genes showed changed expression, indicating that plants seem to adjust themselves to this abiotic stress. Most of the up-regulated genes are already known to be involved in abiotic stress responses and pathogen attacks, especially wounding. However, down-regulated genes for the members of extensins and peroxidases are specific to the acid treatment. These results suggest that acid treatment turns on genes involved in stress responses, especially in wounding and turns off genes very specific for the acid stress.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2023.04a
• /
• pp.157-157
• /
• 2023

Pre-harvest sprouting (PHS) in rice (Oryza sativa L.) is one of the main problems associated with seed dormancy. PHS causes yield loss and reduction of grain quality under unpredictable humid conditions at the ripening stage, thus affecting the economic value of the rice crop. To resolve this issue, it is important to understand the molecular mechanism underlying seed dormancy in rice. Recent studies have shown that seed dormancy is affected by a large number of genes associated with plant hormones. However, the effect of heat stress on seed dormancy and plant hormones is not well understood. In this study, we compared the PHS rate as well as the transcriptome and small RNAome of the seed embryo and endosperm of two different accessions of rice, PHS-susceptible rice (low dormancy) and PHS-resistant rice (high dormancy) under three different maturation stages. We identified and verified the candidate genes associated with seed dormancy and heat stress-related responses in rice using quantitative real-time PCR. We newly discovered hormone-related genes, heat shock protein-related genes, and miRNAs potentially involved in PHS. These findings provide a foundation for understanding the dynamics of transcriptome and small RNAome of hormone- and heat stress-related genes, which affect PHS during seed maturation.

• Korean Journal of Microbiology
• /
• v.52 no.2
• /
• pp.148-156
• /
• 2016

This study examined effects of Enterobacter ludwigii SJR3 showing a high 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, on growth of tomato plant and its expression of stress-related genes under drought and salt stress. SJR3 strain was inoculated at $10^6cell/g$ soil to 4-week grown tomato plants, and drought and salt stresses were treated. After additional incubation for 1 week, root length, stem length, fresh weight and dry weight of tomato plants treated with SJR3 increased by 37.8, 37.2, 96.8 and 146.6%, respectively compared to those of uninoculated plants in drought stress environment, and they increased by 19.2, 25.4, 19.5, and 105.8%, respectively in salt stress environment. Proline content in tomato leaves increased significantly under stress conditions as one of a protecting substance against stresses, but proline contents in tomato treated with SJR3 decreased by 62.1 and 54.1%, respectively. Relative expression of genes encoding ACC oxidase, ACO1 and ACO4, ethylene response factor genes ERF1 and ERF4, and some other stress-related genes were examined from tomato leaves. Compared to the non-stressed tomato, expressions of all stress-related genes increased significantly in the stressed tomato, but gene expressions in the inoculated tomato were similar to those of no-stressed control tomato. Therefore, E. ludwigii SJR3 may play an important role in mitigating drought and salt stress in plants, and can increase productivity of crops under various abiotic stresses.