• Journal of Mushroom
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• v.7 no.4
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• pp.150-155
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• 2009

Because the import of Inonotus obliquus have been rapidly increased in Korea, we developed the Inonotus species-specific marker by using various sequences including ITS sequences, PCR-RFLP and STS primers and used this marker to determine both genetic relatedness and strains discrimination of Inonotus spp. Total 17 different Inonotus spp. were examined by using ITS sequences and classified into 2 different groups. One strain, ASI74008 isolated from Kamchaka island of Siberia, showed the high sequence identity (98%) at the nucleotide level to the other I. obliquus DSM strain, indicating the ASI74008 belong to I. obliquus species. Comparison of banding patterns after restriction enzyme digestions with PCR amplicons of ITS region revealed some variations depending on the species and strains. However, PCR products amplified with STS primer showed species specific patterns.Therefore, use of both STS primers and PCR-RFLP could help for better strain identification.

• Journal of Life Science
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• v.20 no.9
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• pp.1415-1419
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• 2010

Consumption of green tea has increased along with increasing concern regarding healthier lifestyles, and many brands of green tea are sold with a label indicating the region of Korea in which the tea was produced. However, there is little information on identifying the difference between the green tea cultivars according to the region they were grown. Here, 9 green tea cultivars collected from Hadong region, Bosung region, China and Japan were subjected to the STS-RFLP analysis. Using the coding and noncoding DNA regions of genes related to the phenylpropanoid pathway, such as phenylalanine ammonia-lyase, chalcone synthase and dihydroflavonol 4-reductase, we have identified the differences between green tea cultivars according to the region they were grown in. In this study, we showed a STS-RFLP method of green tea analysis which easily distinguished different kinds of tea using the primers as described. In addition, we identified that the green tea cultivars from Hadong and Bosung displayed a different profile when PAL intron was digested with Dde I, suggesting that a rapid authentication system for green tea cultivars grown in different regions in Korea is available.

• Molecules and Cells
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• v.27 no.1
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• pp.21-37
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• 2009

Map-based cloning to find genes of interest, marker-assisted selection (MAS), and marker-assisted breeding (MAB) all require good genetic maps with high reproducible markers. For map construction as well as chromosome assignment, development of single copy PCR-based markers and map integration process are necessary. In this study, the 132 markers (57 STS from BAC-end sequences, 13 STS from RFLP, and 62 SSR) were newly developed as single copy type PCR-based markers. They were used together with 1830 markers previously developed in our lab to construct an integrated map with the Joinmap 3.0 program. This integrated map contained 169 SSR, 354 RFLP, 23 STS from BAC-end sequences, 6 STS from RFLP, 152 AFLP, 51 WRKY, and 99 rRAMP markers on 12 chromosomes. The integrated map contained four genetic maps of two interspecific (Capsicum annuum 'TF68' and C. chinense 'Habanero') and two intraspecific (C. annuum 'CM334' and C. annuum 'Chilsungcho') populations of peppers. This constructed integrated map consisted of 805 markers (map distance of 1858 cM) in interspecific populations and 745 markers (map distance of 1892 cM) in intraspecific populations. The used pepper STS were first developed from end sequences of BAC clones from Capsicum annuum 'CM334'. This integrated map will provide useful information for construction of future pepper genetic maps and for assignment of linkage groups to pepper chromosomes.

• Journal of Korean Society of Water and Wastewater
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• v.26 no.6
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• pp.767-777
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• 2012

Annular Biofilm Reactor (ABR) equipped with coupons of three different pipe materials (STS 304, PVC, PE) was used to generate drinking water biofilm samples. The level of assimilable organic carbon (AOC) during the sample generation period was $37.3{\mu}g/L$, and this level did not seem to be low enough to limit the formation of biofilm in this study. Terminal-restriction fragment length polymorphism (T-RFLP) analyses determined T-RF profile as early as 3 h of exposure on PVC coupons. Average surface roughness ($R_a$) measured by atomic force microscopic analyses was 125.7 nm for PVC, and this value was higher than for STS (71.6 nm) and PE (74.0 nm). However, biofilm formation was faster on STS (6 h) than on PE (12 h), which indicated that surface roughness might not be the only factor that controlled the initiation of biofilm development. Upon detection of the T-RF peaks, richness (S) and diversity indices such as Shannon (H) and Simpson (1/D) demonstrated a rather slow increase until 48 h followed by rapid increase regardless of the pipe materials. Differences of microbial community structures among the biofilm samples were determined based on the cluster analysis using Jaccard coefficients (Sj). Biofilm communities could be divided into two distinct groups according to the exposure time regardless of the pipe materials. First group contained a young (< 48 h) biofilm samples (10 out of 11) but second group contained a mature (${\geq}$ 48 h) samples (11 out of 14). Results suggested that, due to the complexity of biofilm, the targeting of the first group of cluster was crucial for optimizing the management of drinking water distribution systems and controlling microbial growth.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.44 no.4
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• pp.345-349
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• 1999

This study was carried out to map Bphl and bph2 gene in Mudgo and Sangju13 (Oryza sativa L.) respectively conferring resistance to brown plan-thopper (BPH) and to establish the marker-assisted selection (MAS) system. Bulked seedling (grown for 20 days) test was conducted with the 73 F4 lines derived from a cross between Nagdongbyeo and Mudgo for Bphl and with 53 BC3F5 lines derived from the Milyang95/Sangju13 cross for bph2. Bph1 was mapped between RG413 and RG901 on chromo-some 12 at a distance of 7.5 cM from RG413 and 8.4 cM from RG90l. A recessive gene bph2 was located near RZ76 on chromosome 12 at a distance of 14.4 cM. Bphl and bph2 were linked to each other with a distance of about 30 cM. An RFLP marker, RG413 linked to Bphl, was converted to an STS marker to facilitate the marker-assisted selection. BPH resistant genotypes could be selected with 92% accuracy in a population derived from a line of NM47-B-B.

• Genomics & Informatics
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• v.5 no.4
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• pp.194-195
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• 2007

We have constructed the Rice Genome Information Service System (RGISS), which is an information service system of the Oryza sativa L. ssp. japonica (rice) genome, using the released version of rice Build 3.0 pseudomolecules based on the Ensembl architecture. The nonredundant library, composed of 3,360 clones of BACs, PACs, and fosmids, was used to construct supercontigs. RGISS contains 50,717 annotated genes from GenBank, 56,161 predicted genes from FgeneSH, and information on 9,587 markers, which includes STS, SSR, and EST-based RFLP. The 20,180 ESTs sequenced by the Korea National Institute of Agricultural Biotechnology (NIAB) were aligned and mapped into 168,792 exons. By gene ontology analysis, the classified protein numbers in the rice genome were 6158, 4531, and 12,364 proteins, which were mapped to molecular function, cellular component, and biological process, respectively.

• Molecules and Cells
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• v.19 no.3
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• pp.318-327
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• 2005

Southern blot analysis revealed a ubiquitous distribution and high copy number of Ty3-gypsy-like elements in the genome of Hibiscus syriacus. Comparative phylogenetic analysis of the large subunit of Rubisco and the integrase region of Ty3-gypsy elements in various plant species indicated that the retrotransposon-like sequences have different evolutionary histories and their own unique polymorphism in the H. syriacus population. Sequence-tagged site-restriction fragment length polymorphisms (STS-RFLP) analysis also indicated great variability in the numbers and sequences of Ty3-gypsy-like elements within H. syriacus varieties. Ty3-gypsy-like elements may still be active within H. syriacus, since Northern analysis of wounded leaves of H. syriacus variety Saehan with a probe for the integrase domain gave strong hybridization signals. The sequence heterogeneity and ubiquity of the Ty3-gypsy-like elements in H. syriacus genomes could provide reliable DNA markers for line identification as well for the analysis of genetic diversity in H. syriacus.