• The Korean Journal of Malacology
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• v.30 no.3
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• pp.197-210
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• 2014

Single nucleotide polymorphisms (SNPs) are widely acknowledged as the marker of choice for many genetic and genomic applications because they show co-dominant inheritance, are highly abundant across genomes and are suitable for high-throughput genotyping. Here we evaluated the applicability of SNP markers developed from Crassostrea gigas and C. virginica expressed sequence tags (ESTs) in closely related Crassostrea and Ostrea species. A total of 213 putative interspecific level SNPs were identified from re-sequencing data in six amplicons, yielding on average of one interspecific level SNP per seven bp. High polymorphism levels were observed and the high success rate of transferability show that genic EST-derived SNP markers provide an efficient method for rapid marker development and SNP discovery in closely related oyster species. The six EST-SNP markers identified here will provide useful molecular tools for addressing questions in molecular ecology and evolution studies including for stock analysis (pedigree monitoring) in related oyster taxa.

• Journal of fish pathology
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• v.22 no.3
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• pp.383-389
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• 2009

Analysis of expressed sequence tags (ESTs) is an efficient approach for gene discovery, expression profiling, and development of resources useful for functional genomics studies. As part of studies on the immune system of olive flounder, a total of 251 EST sequences from gill cDNA library were generated to identify and characterize important genes in the immune machanisms of olive flounder. Of the 251 clones, 126 clones (50.2%) were identified as orthologues of known genes from olive flounder and other organisms. Among the 126 EST clones, 16 clones (12.7%) were representing 9 unique genes identified as homologous to the previously reported olive flounder ESTs, 100 clones (79.4%) representing 103unique genes were identified as orthologs of known genes from other organisms. We also identified several kinds of immune associated proteins, indicating EST as a powerful method for identifying immune related genes of fish as well as identifying novel genes. Further studies using cDNA microarrays are needed to identify the differentially expressed transcripts after disease infection.

• Journal of Microbiology and Biotechnology
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• v.22 no.7
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• pp.902-906
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• 2012

Expressed sequence tags (ESTs) from the Antarctic green algae Pyramimonas gelidicola were analyzed to obtain molecular information on cold acclimation of psychrophilic microorganisms. A total of 2,112 EST clones were sequenced, generating 222 contigs and 219 singletons, and 200 contigs and 391 singletons from control ($4^{\circ}C$) and cold-shock conditions ($-2^{\circ}C$), respectively. The complete EST sequences were deposited to the DDBJ EST database (http://www.ddbj.nig.ac.jp/index-e.html) and the nucleotide sequences reported in this study are available in the DDBJ/EMBL/GenBank. These EST databases of Antarctic green algae can be used in a wide range of studies on psychrophilic genes expressed by polar microorganisms.

• Korean Journal of Medicinal Crop Science
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• v.21 no.6
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• pp.444-454
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• 2013

The development of random amplified polymorphic DNA (RAPD) and expressed sequence tag-derived simple sequence repeats (EST-SSRs) provided a useful tool for investigating Korean ginseng genetic diversity. In this study, 18 polymorphic markers (7 RAPD and 11 EST-SSR) selected to assess the genetic diversity in 31 ginseng accessions (11 Korean ginseng cultivars and 20 breeding lines). In RAPD analysis, a total of 53 unique polymorphic bands were obtained from ginseng accessions and number of amplicons ranged from 4 to 11 with a mean of 7.5 bands. Pair-wise genetic similarity coefficient (Nei) among all pairs of ginseng accessions varied from 0.01 to 0.32, with a mean of 0.11. On the basis of the resulting data, the 31 ginseng accessions were grouped into six clusters. As a result of EST-SSR analysis, 11 EST-SSR markers detected polymorphisms among the 31 ginseng accessions and revealed 49 alleles with a mean of 4.45 alleles per primer. The polymorphism information content (PIC) value ranged from 0.06 to 0.31, with an average of 0.198. The 31 ginseng accessions were classified into five groups by cluster analysis based on Nei's genetic distances. Consequently, the results of ginseng-specific RAPD and EST-SSR markers may prove useful for the evaluation of genetic diversity and discrimination of Korean ginseng cultivars and breeding lines.

• International Journal of Ocean System Engineering
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• v.2 no.1
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• pp.37-49
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• 2012

An analysis of potential flooding by storm surge and wave run-up and overtopping can be used to evaluate protection afforded by the existing storm protection system. The analysis procedure can also be used to evaluate various protection alternatives for providing typhoon flood protection. To determine risk, the storm surges for both historical and hypothetical are compiled with tide conditions to represent high, slack and low water for neap, spring and mid range tides to use with the statistical procedure known as the Empirical Simulations Technique (EST). The EST uses the historic and hypothetical events to generate a large population of life-cycle databases that are used to compute mean value maximum storm surge elevation frequency relationships. The frequency-of-occurrence relationship is determined for all relevant locations along the shoreline at appropriate locations to identify the effect using the Empirical Storm Simulation (EST). To assist with understanding the process, an example is presented for a study of storm surge analysis for Freeport, Texas. This location is in the Gulf of Mexico and is subject to hurricanes and other tropical storms that approach from the Atlantic Ocean.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2003.04a
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• pp.121-121
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• 2003

Expressed sequence tags (EST) are help to quickly identify functions of expressed genes and to understand the complexity of gene expression. To assist genetic study of the root development in Panax ginseng, which is one of the most important medicinal plant, expressed sequence tags (EST) analysis was carried out. We constructed a CDNA library using the 4-year Chunpoon root. Partial sequences were obtained from 3,841 clone. The ESTs could be clustered into 2,056 (64%) non-redundant groups. Similarity search of the non-redundant ESTs against public non-redundant databases of both protein and DNA indicated that 1,498 groups show similarity to genes of known function. These ESTs clones were divided into eighteen categories depending upon gene function. The most abundant transcripts were major latex protein (41), ribonuclease 2 (36), metallothionein 2(35). Our extensive EST analysis of genes expressed in 4-year Chunpoong root not only contributes to the understanding of the dynamics of genome expression patterns in root organ development but also adds data to the repertoire of all genomic genes.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2020.08a
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• pp.47-47
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• 2020

The Korean National Agrobiodiversity Center holds the more than 1300 accessions of proso millet, but a large portion of accessions are landrace of Korea that has very similar traits. To comprehend the maximum genetic diversity of this crop, a core collection with minimum number of accessions will facilitate easy access to genetic material. Here we assessed the genetic diversity and population structure in a germplasm collection of 830 accessions by employing EST-SSR markers and morphological traits. A total of 107 alleles were detected with an average allele number of 4.9 per locus among the 830 accessions based on 37 EST-SSR markers. The number of alleles per locus ranged from 2 to 7. Polymorphism information content and expected heterozygosity ranged from 0.06 to 0.68 (mean = 0.21) and 0.06 to 0.73 (mean = 0.23), respectively. The germplasm collection was separated into two groups based on population structure analysis, whereas principal coordinate analysis (PCoA) could not cluster accessions according to their geographic origin. Subsequently, a preliminarily developed core collection with a total of 141 accessions (17%) was selected from the whole set of germplasm by combining allelic variations of EST-SSR markers and eight different phenotypic traits. The core collection optimally represented the whole germplasm collection and displayed a similar level of PCoA value and genetic variation from the initial collection. The results obtained here provide a primary resource for further genetic analysis and establish a reference for further development of appropriate genetic breeding strategies.

• KSCE Journal of Civil and Environmental Engineering Research
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• v.29 no.2B
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• pp.141-153
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• 2009

The occurrence causes of the extreme rainfall to happen in Korea can be distinguished with the typhoons and local downpours. The typhoon events attacked irregularly to induce the heavy rainfall, and the local downpour events mean a seasonal rain front and a local rainfall. Almost every year, the typhoons and local downpours that induced a heavy precipitation be generated extreme disasters like a flooding. Consequently, in this research, There were distinguished the causes of heavy rainfall events with the typhoons and the local downpours at Korea. Also, probability precipitation was computed according to the causes of the local downpour events. An evaluation of local downpours can be used for analysis of heavy rainfall event in short period like a flash flood. The methods of calculation of probability precipitation used the parametric frequency analysis and the Empirical Simulation Technique (EST). The correlation analysis was computed between annual maximum precipitation by local downpour events and sea surface temperature, moisture index for composition of input vectors. At the results of correlation analysis, there were revealed that the relations closely between annual maximum precipitation and sea surface temperature. Also, probability precipitation using EST are bigger than probability precipitation of frequency analysis on west-middle areas in Korea. Therefore, region of west-middle in Korea should prepare the extreme precipitation by local downpour events.

• Journal of fish pathology
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• v.23 no.3
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• pp.429-440
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• 2010

We constructed a rock bream (Oplegnathus fasciatus) gill cDNA library and a total of 1450 expressed sequence tag (EST) clones were generated. Gene annotation procedures and homology searches of the sequenced ESTs were locally done by BLASTX for amino acid similarity comparisons. Of the 1450 EST clones, 1022 EST clones showed significant homology to previously described genes while 428 ESTs were unidentified, and 259 clones were hypothetical, or unnamed proteins. Encoding 313 different sequences were identified as putative bio-defense genes or genes associated with immune response.

• Journal of fish pathology
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• v.23 no.2
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• pp.229-238
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• 2010

We constructed a rock bream (Oplegnathus fasciatus) liver cDNA library and a total of 1533 expressed sequence tag (EST) clones were generated. Gene annotation procedures and homology searches of the sequenced ESTs were analyzed using BLASTX. Of the 1533 EST clones, 1165 different ESTs showed significant homology to previously described genes while 368 ESTs were unidentified, hypothetical, or unnamed proteins. Encoding 106 different sequences were identified as putative bio-defense genes or genes associated with immune response.