• KOREAN JOURNAL OF CROP SCIENCE
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• v.57 no.1
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• pp.71-77
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• 2012

The objective of this study is to develop the gene based sequence tagged site (STS) markers in wheat. The euchromatin enriched genomic library was constructed and the STS primer sets were designed using gene based DNA sequence. The euchromatin enriched genomic (EEG) DNA library in wheat was constructed using the $Mcr$A and $Mcr$BC system in $DH5{\alpha}$ cell. The 2,166 EEG colonies have been constructed by methylated DNA exclusion. Among the colonies, 606 colonies with the size between 400 and 1200 bp of PCR products were selected for sequencing. In order to develop the gene based STS primers, blast analysis comparing between wheat genetic information and rice genome sequence was employed. The 227 STS primers mainly matched on $Triticum$ $aestivum$ (hexaploid), $Triticum$ $turgidum$ (tetraploid), $Aegilops$ (diploid), and other plants. The polymorphisms were detected in PCR products after digestion with restriction enzymes. The eight STS markers that showed 32 polymorphisms in twelve wheat genotypes were developed using 227 STS primers. The STS primers analysis will be useful for generation of informative molecular markers in wheat. Development of gene based STS marker is to identify the genetic function through cloning of target gene and find the new allele of target trait.

• Animal Systematics, Evolution and Diversity
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• v.36 no.4
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• pp.347-353
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• 2020

Although sea slaters Ligia have a significant role in rocky shore habitats, their taxonomic entities have not been clearly understood. In this study, we investigated whether genetic variation inferred from a nuclear genetic marker, namely amplified fragment length polymorphism (AFLP), would conform to that of a mitochondrial DNA marker. Using both the mitochondrial DNA marker and the AFLP marker amplified by the six selective primer sets, we analyzed 95 Ligia individuals from eight locations from East Asia. The direct sequencing of mitochondrial 16S rRNA gene revealed three distinct genetic lineages, with 9.8-11.7 Kimura 2-parameter genetic distance. However, the results of AFLP genotyping analysis with 691 loci did not support those of mitochondrial DNA, and revealed an unexpectedly high proportion of shared polymorphisms among lineages. The inconsistency between the two different genetic markers may be explained by difference in DNA evolutionary history, for example inheritance patterns, effective population size, and mutation rate. The other factor is a possible genomic island of speciation, in that most of the genomic parts are shared among lineages, and only a few genomic regions have diverged.

• Biomolecules & Therapeutics
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• v.3 no.2
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• pp.154-158
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• 1995

We isolated Streptomyces spry. from Korean soil, which showed high cytotoxicity against tumor cell lines, L1210 and P388Dl. Among 30 strains, three strains (DKM 104, DKM 128, DKM 409) were appeared to possess plasmid. Strain DKM 104 and DKM 128 had two CCC(Covalently Closed Circular) form plasmid, about 20 Kb in size and about 1 Kb compared with λ Hind III DNA size marker. And strain DKM 409 had three plasmids, among which two plasmic were CCC form about 20 Kb and about 20 Kb compared with same size marker. To find out whether plasmid involved in production of antitumor agent or not, we performed to curing experiment. Comparing cytotoxicity between culture filtrate of plasmid-containing strains and cured strains, we knew that only the cytotoxic activity of the strain DKM 128 was involved in plasmid.

• Journal of the Institute of Electronics Engineers of Korea SP
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• v.42 no.6
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• pp.33-42
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• 2005

In this paper, we propose an efficient segmentation algerian using morphological grayscale reconstruction for region-based coding. Each segmentation stage consists of simplification, marker extraction and decision. The simplification removes unnecessary components to make an easier segmentation. The marker extraction finds the flat zones which are the seed points from the simplified image. The decision is to locate the contours of regions detected by the marker extraction. For the simplification, we use a new connected operator based on the size and contrast. In the marker extraction stage, the regions reconstructed to original values we excluded from the candidate marker. For the other regions, the regions which are larger than structuring elements or have higher contrast than a threshold value are selected as markers. For the initial segmentation, the conventional hierarchical watershed algorithm and the extracted markers are used. Finally in the region merging stage, we propose an efficient region merging algorithm which preserves a high quality in terms of the number of regions. At the same time, the pairs which have higher contrast than a threshold are excluded from the region merging stage. Experimental results show that the proposed marker extraction method produces a small number of markers, while maintaining high quality and that the proposed region merging algorithm achieves a good performance in terms of the image quality and the number of regions.

• Proceedings of the Korean Society for Food Science of Animal Resources Conference
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• 2000.11a
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• pp.59-75
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• 2000

This study was carried out to develop a DNA marker for identifying between Korean cattle (Hanwoo) and other breeds. First experiment was performed to isolate Hanwoo specific DNA marker at sequence characterized amplified regions (SCARs). Five breeds of cattle including Hanwoo, Holstein, Hereford, Angus and Charolais were represented with the from 8 to 20 individuals. Fourteen primers of 300 arbitrary primers of 10 nucleotides showed reproducible polymorphism across the breeds. An amplified band of 0.9 kb in the primer MG-3 showed the specificity to Holstein breed. And MG-6 and MG-12 detected the Hereford and Hanwoo specific markers at the size of 2.0 kb and 1.0 kb, respectively. A 1.0 kb band of MG-12 was cloned and sequenced. A SCAR primer was designed based on the obtained sequences. It was possible to identify the Hanwoo from Holstein breed. Second experiment was carried out to observe the genotype frequencies of MC1R in 1,044 samples of imported beef and eight different cattle breeds including Hanwoo, Holstein, Angus, Brown-Swiss, Charolais, Limousin, Simmental and Hereford. The primers for the amplification of bovine MC1R gene were designed based on a bovine MC1R gene sequence (GenBank accession no.Y19103). A size of 350 bp was amplified by polymerase chain reaction(PCR), digested with two different restriction enzyme, BsrFI and MspA II, and electrophoresed in 2.5% Metaphore agarose gel for determination of genotypes. Genotype frequencies of Hanwoo were 0.10 in E+e and 0.90 in ee. Allele ED was shown in all of Holstein and Angus breeds tested which have black coat color phenotypes. We suggested that SCAR marker and the bovine MC1R gene could be used as a DNA marker for distinguishing beef between Hanwoo and Holstein.

• Journal of Life Science
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• v.15 no.3 s.70
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• pp.474-478
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• 2005

This study was conducted to analyze genetic characteristics and to develop the specific marker for Cheju native horse (Coo) at the level of sequence characterized amplified regions (SCARs). We collected blood samples from Cheju native horse and Thoroughbred horse (Th) and obtained genomic DNA from the blood of 50 individuals randomly selected within the breeds. Seven hundred primers were chosen randomly and were used to examin the polymorphism and 40 kinds of primers showed polymorphic RAPD band patterns between two breeds. Thirty primers of them showed horse specific bands. With the primer MG 30, amplified band of 2.0 kb showed the specificity to Cheju native horse (Cnh). Additionally MG 53 detected the thoroughbred horse (Th) specific markers at size of 2.3 kb. As the next, 2.3 kb band from MG 53 was checked with the all individuals from all the breeds of this study, and it maintained the reproducible breed specificity to thoroughbred horse (Th). With this results, 2.3 kb band was cloned into plasmid vector and sequenced bidirectionally from both ends of the cloned fragment. With the obtained sequences 10 nucleotide extended primers including the original arbitray primer were designed as a SCARs primer. Finally, the primer with extended sequence showed the reproducible breed differentiation pattern and it was possible to identify Cheju native horse (Cnh) from other breeds. The SCARs marker 2.3 kb from MG 53 could be used to identify Cheju native horse (Cnh) for not only registration but also horse breeding programe.

• Journal of Mushroom
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• v.11 no.3
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• pp.171-176
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• 2013

Genomic DNAs of psychrophilic strains of Pleurotus eryngii were analyzed by randomly amplified polymorphic DNA (RAPD) using OP-A, OP-B, OP-L, OP-P, OP-R and OP-S3 primers to develop the strain-specific DNA marker. A unique DNA fragment with the size of 480 bp was yielded by OP-S3 primer from the psychrophilic strain. A sequence characterized amplified region (SCAR) marker, designated as OP-S3-1, was designed on the basis of the determined sequence. The PCR analysis with the OP-S3-1 primer showed that this SCAR marker can clearly distinguish the psychrophilic strains from the control strains.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.48 no.5
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• pp.413-418
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• 2003

Genetic diversity and soybean sprout-related traits were evaluated in a total of 72 soybean accessions (60 Glycine max, 7 Glycine soja, and 5 Glycine gracilis). 100-seed weight (SW) was greatly varied and ranged from 3.2g to 32.3g in 72 soybean accessions. Positive correlation was observed between GR and hypocotyl length (HL), whereas negative correlation was observed between SW and hypocotyl diameter (HD). Re-evaluation by discarding two soybean genotypes characterized with low GR indicated that much higher correlation of sprout yield (SY) with HD and SW. Based on the principal component analysis (PCA) for sprout-related traits, 57 accessions were classified. Soybean genotypes with better traits for sprout, such as small size of seeds and high SY, were characterized with high PCA 1 and PCA 2 values. The seed size in second is small but showed low GR and SY, whereas the third has large seed, high GR and more than 400% SY. In genetic similarity analysis using 60 SSR marker genotyping, 72 accessions were classified into three major and several minor groups. Nine of twelve accessions that were identified as the representatives of soybean for sprout based on PCA were in a group by the SSR marker analysis, indicating the SSR marker selection of parental genotypes for soybean sprout improvement program.

• ALGAE
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• v.33 no.1
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• pp.49-54
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• 2018

Red algal mitochondrial genomes (mtDNAs) can provide useful information on species identification. mtDNAs of Pyropia / Porphyra (Bangiales, Rhodophyta) have shown diverse variation in their size and gene structure. In particular, the introns and intronic open reading frames found in the ribosomal RNA large subunit gene (rnl) and cytochrome c oxidase subunit 1 gene (cox1) significantly vary the mitochondrial genome size in Pyropia / Porphyra species. In this study, we examined the exon / intron structure of rnl and cox1 genes of Pyropia yezoensis at the intraspecific level. The combined data of rnl and cox1 genes exhibited 12 genotypes for 40 P. yezoensis strains, based on the existence of introns. These genotypes were more effective to identify P. yezoensis strains in comparison to the traditional DNA barcode cox1 marker (5 haplotypes). Therefore, the variation in gene structure of rnl and cox1 can be a novel molecular marker to discriminate the strains of Pyropia species.

• Ocean Science Journal
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• v.40 no.3
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• pp.145-153
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• 2005

Variation in the microbial biomass and community structure found in sediment of heavily polluted bays and the adjacent unpolluted areas were examined using phospholipid fatty acid analysis. Total microbial biomass and microbial community structure were responding to environmental determinants, sediment grain size, depth of sediment, and pollution due to petroleum hydrocarbons. The marker fatty acids of microeukaryotes and prokaryotes - aerobic, anaerobic, and sulfate-reducing bacteria - were detected in sediments of the areas studied. Analysis of the fatty acid profiles revealed wide variations in the community structure in sediments, depending on the extent of pollution, sediment depth, and sediment grain size. The abundance of specific bacterial fatty acids points to the dominance of prokaryotic organisms, whose composition differed among the stations. Fatty acid distributions in sediments suggest the high contribution of aerobic bacteria. Sediments of polluted sites were significantly enriched with anaerobic bacteria in comparison with clean areas. The contribution of this bacterial group increased with the depth of sediments. Anaerobic bacteria were predominantly present in muddy sediments, as evidenced from the fatty acid profiles. Relatively high concentrations of marker fatty acids of sulfate-reducing bacteria were associated with organic pollution in this site. Specific fatty acids of microeukaryotes were more abundant in surface sediments than in deeper sediment layers. Among the microeukaryotes, diatoms were an important component. Significant amounts of bacterial biomass, the predominance of bacterial biomarker fatty acids with abundance of anaerobic and sulfate-reducing bacteria are indicative of a prokaryotic consortium responsive to organic pollution.