• Korean Journal of Plant Resources
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• v.29 no.3
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• pp.322-330
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• 2016

Understanding the genetic variation among landrace collections is important for crop improvement and utilization of valuable genetic resources. The present study was carried out to analyse the genetic diversity and associated population structure of 621 foxtail millet accessions of Korean landraces using 22 EST-SSR markers. A total of 121 alleles were detected from all accessions with an average of 5.5 alleles per microsatellite locus. The average values of gene diversity, polymorphism information content, and expected heterozygosity were 0.518, 0.594, and 0.034, respectively. Following the unweighted neighbor-joining method with arithmetic mean based clustering using binary data of polymorphic markers, the genotypes were grouped into 3 clusters, and population structure analysis also separated into 3 populations. Principal coordinate analysis (PCoA) explained a variation of 13.88% and 10.99% by first and second coordinates, respectively. However, in PCoA analysis, clear population-level clusters could not be found. This pattern of distribution might be the result of gene flow via germplasm exchanges in nearby regions. The results indicate that these Korean landraces of foxtail millet exhibit a moderate level of diversity. This study demonstrated that molecular marker strategies could contribute to a better understanding of the genetic structure in foxtail millet germplasm, and provides potentially useful information for developing conservation and breeding strategies.

• BMB Reports
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• v.37 no.4
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• pp.474-479
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• 2004

The expressed sequence tag (EST) effort in Toxoplasma gondii has generated a substantial amount of gene information. To exploit this valuable resource, we chose to study tgd057, a novel gene identified by a large number of ESTs that otherwise show no significant match to known sequences in the database. Northern analysis showed that tgd057 is transcribed in this tachyzoite. The complete cDNA sequence of tgd057 is 1169 bp in length. Sequence analysis revealed that tgd057 possibly adopts two polyadenylation sites, utilizes the fourth in-frame ATG for translation initiation, and codes for a secretory protein. The longest open reading frame for the tgd057 gene was cloned and expressed as a recombinant protein (rd57) in Escherichia coli. Western analysis revealed that serum against rd57 recognized a molecule of ~21 kDa in the tachyzoite protein extract. This suggests that the tgd057 gene is expressed in vivo in the parasite.

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.11a
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• pp.316-316
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• 2005

• Korean Journal of Agricultural Science
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• v.38 no.1
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• pp.11-16
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• 2011

In this study, we report the generation and analysis of a total of 1,211 expressed sequence tags (ESTs) from Pinus koraiensis. A cDNA library was generated from the young leaf tissue and a total of 1,211 cDNA were partially sequenced. EST and unigene sequence quality were determined by computational filtering, manual review, and BLAST analyses. In all, 857 ESTs were acquired after the removal of the vector sequence and filtering over a minimum length 50 nucleotides. A total of 411 unigene, consisting of 89 contigs and 322 singletons, was identified after assembling. Also, we identified 77 new microsatellite-containing sequences from the unigenes and classified the structure according to their repeat unit. According to homology search with BLASTX against the NCBI database, 63.1% of ESTs were homologous with known function and 22.2% of ESTs were matched with putative or unknown function. The remaining 14.6% of ESTs showed no significant similarity to any protein sequences found in the public database. Gene ontology (GO) classification showed that the most abundant GO terms were transport, nucleotide binding, plastid, in terms biological process, molecular function and cellular component, respectively. The sequence data will be used to characterize potential roles of new genes in Pinus and provided for the useful tools as a genetic resource.

• Proceedings of the Korean Society of Plant Pathology Conference
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• 2003.10a
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• pp.67.1-67
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• 2003

Phytophthora blight is a devastating disease of pepper and occurs almost anywhere peppers are grown. Phytophthora blight is caused by Phytophthora capsici and this pathogen can infect every part of the plant by moving inoculum in the soil, by infecting water on surface, by aerial dispersal to sporulating lesions. Management of Phytophthora blight currently relies on cultural practices, crop rotation, and use of selective fungicides. Since these treatments are a short-term management, a classical breeding for development of resistant pepper against the Phytophthora is an alternative. So far some of the resistant cultivars have been on the market, but those are limited regionally and commercially. Therefore, ultimately an elite line resistant against this disease should be developed, if possible, by biotechnology. We have set out a series of work recently in order to develop Phytophthora resistant pepper cultivar. For the first time, the cDNA microarray analysis was peformed using an EST chip that holds around 5000 pepper EST clones to identify genes responsive to Phytophthora infection. Total RNA samples were obtained from Capsicum annuum PI201234 after inoculating P. capsici to roots and soil and exposed to the chip. .Around 900 EST clones were up-regulated and down-regulated depending on the two RNA sample tissues, leaf and root. From those, we have found 55 transcription factors that may be involved in gene regulation of the disease defense mechanism. Further and in detail information will be provided in the poster.

• Journal of Life Science
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• v.24 no.11
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• pp.1187-1192
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• 2014

Pepper, consumed as a typical spice food around world, is mainly cultivated in warm countries, including Korea, China, and Mexico. Phytophthora capsici is a pathogen on several economically important crops, including pepper. The oomycete attacks the roots, stems, leaves, and fruit of the host plants. To understand the molecular mechanisms underlying development of the disease, the genes expressed during pepper-P. capsici interaction were explored by analyzing expressed sequence tags (ESTs). A cDNA library was constructed from total RNA extracted from pepper leaves challenged with P. capsici for three days, resulting in an early stage of symptom development for comparable interaction. A comprehensive analysis of single-pass sequencing of 5,760 randomly selected cDNA clones extracted 5,148 high-quality entries for contig assembly, which generated 2,990 unigenes. A homology search of the unigenes with BLASTX resulted in 2,409 matches, of which 606 showed classified functional catalogs.

• BMB Reports
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• v.39 no.2
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• pp.183-188
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• 2006

Using the Phred/Phrap/Polyphred/Consed pipeline established in the National Livestock Research Institute of Korea, we predicted candidate coding single nucleotide polymorphisms (cSNPs) from 7,600 expressed sequence tags (ESTs) derived from three cDNA libraries (liver, M. longissimus dorsi, and intermuscular fat) of Hanwoo (Korean native cattle) steers. From the 7,600 ESTs, 829 contigs comprising more than two EST reads were assembled using the Phrap assembler. Based on the contig analysis, 201 candidate cSNPs were identified in 129 contigs, in which transitions (69%) outnumbered transversions (31%). To verify whether the predicted cSNPs are real, 17 SNPs involved in lipid and energy metabolism were selected from the ESTs. Twelve of these were confirmed to be real while five were identified as artifacts, possibly due to expressed sequence tag sequence error. Further analysis of the 12 verified cSNPs was performed using the program BLASTX. Five were identified as nonsynonymous cSNPs, five were synonymous cSNPs, and two SNPs were located in 3'-UTRs. Our data indicated that a relatively high SNP prediction rate (71%) from a large EST database could produce abundant cSNPs rapidly, which can be used as valuable genetic markers in cattle.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.11
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• pp.1555-1565
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• 2009

Anaerobic rumen fungi have been regarded as good genetic resources for enzyme production which might be useful for feed supplements, bio-energy production, bio-remediation and other industrial purposes. In this study, an expressed sequence tag (EST) library of the rumen anaerobic fungus Neocallimastix frontalis was constructed and functional genes from the EST library were analyzed to elucidate carbohydrate metabolism of anaerobic fungi. From 10,080 acquired clones, 9,569 clones with average size of 628 bp were selected for analysis. After the assembling process, 1,410 contigs were assembled and 1,369 sequences remained as singletons. 1,192 sequences were matched with proteins in the public data base with known function and 693 of them were matched with proteins isolated from fungi. One hundred and fifty four sequences were classified as genes related with biological process and 328 sequences were classified as genes related with cellular components. Most of the enzymes in the pathway of glucose metabolism were successfully isolated via construction of 10,080 ESTs. Four kinds of hemi-cellulase were isolated such as mannanase, xylose isomerase, xylan esterase, and xylanase. Five $\beta$-glucosidases with at least three different conserved domain structures were isolated. Ten cellulases with at least five different conserved domain structures were isolated. This is the first solid data supporting the expression of a multiple enzyme system in the fungus N. frontalis for polysaccharide hydrolysis.

• Journal of Korean Society of Coastal and Ocean Engineers
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• v.21 no.3
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• pp.254-265
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• 2009

The estimation of the extreme sea level is necessary in the design of offshore or coastal structures. In this paper, the storm surge data calculated numerically at 52 harbors around the Korean Peninsula are analyzed by using annual maximum series(AMS), peaks over threshold(POT) and empirical simulation technique(EST). The maximum likelihood method was used to estimate the parameters in both AMS and POT models. The Generalized Pareto distribution was used and Chi-square and Kolmogorov-Smirnov goodness-of-fit tests were performed with the acceptable significance level 5%. The extreme sea levels were also evaluated by EST including tide effect, showing similar results as given by Jeong et al.(2008).

• Genomics & Informatics
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• v.3 no.3
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• pp.86-93
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• 2005

Human brain EST data provide important clues for our understanding of the molecular biology associated with the function of the normal brain and the molecular pathophysiology with brain disorders. To systematically and efficiently study the function and disorders of the human brain, 45,773 human brain ESTs were collected from 27 human brain cDNA libraries, which were constructed from normal brains and brain disorders such as brain tumors, Parkinson's disease (PO) and epilepsy. An analysis of 45,773 human brain ESTs using our EST analysis pipeline resulted in 38,396 high-quality ESTs and 35,906 ESTs, which were coalesced into 8,246 unique gene clusters, showing a significant similarity to known genes in the human RefSeq, human mRNAs and UniGene database. In addition, among 8,246 gene clusters, 4,287 genes ($52\%$) were found to contain full-length cONA clones. To facilitate the extraction of useful information in collected these human brain ESTs, we developed a user-friendly interface system, the Korea Brain Unigene Database (KBUD). The KBUD web interface allows access to our human brain data through three major search modes, the BioCarta pathway, keywords and BLAST searches. Each result when viewed in KBUD offers comprehensive information concerning the analyzed human brain ESTs provided by our data as well as data linked to various other publiC databases. The user-friendly developed KBUD, the first world-wide web interface for human brain EST data with ESTs of human brain disorders as well as normal brains, will be a helpful system for developing a better understanding of the underlying mechanisms of the normal brain well as brain disorders. The KBUD system is freely accessible at http://kugi.kribb.re.kr/KU/cgi -bin/brain. pI.