• Korean Journal of Plant Taxonomy
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• v.42 no.3
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• pp.215-221
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• 2012

Five Korean Calanthe species, C. discolor, C. bicolor, C. sieboldii, C. reflexa, and C. aristulifera, were studied using amplified fragment length polymorphism (AFLP) to assess their taxonomic and genetic relationships. Sixteen accessions belonging to five native Calanthe spp. and mutants with yellow tepal and white lip (YW mutants) were studied. We identified 50 putative markers using AFLP analysis. The results of AMOVA showed that genetic variance was higher between species than within species. Genetic dissimilarity when compared with the rest of the species was the lowest for individuals of the YW mutants and the highest for individuals of C. reflexa. The mutants clustered outside the major group. Calanthe bicolor clustered with C. discolor, suggesting that its genetic composition is closer to that of C. discolor. Though it is suggested to have originated as a result of natural hybridization between C. sieboldii and C. discolor, introgression is likely to have occurred in the direction of C. discolor based on the data of molecular marker, clustering and genetic dissimilarity. Calanthe reflexa and C. aristulifera were genetically the most diverse of the species studied. In conclusion, the results showed that there is genetic diversity in Korean Calanthe species, that C. bicolor introgressed in the direction of C. discolor and that the YW mutants are genetically closer to C. sieboldii.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.41 no.2
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• pp.94-101
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• 2008

In Korean waters, there are two color types (blue and purple) of the blue crab Portunus trituberculatus. The blue type is common, but the ratio of the purple type has increased in landings. To determine whether there were significant morphometric or genetic differences between the blue and purple types, crabs caught from the West Sea of Korea were examined. Based on covariance analysis, there were significant differences in 1 of 10 morphometric characteristics of males between the two types, in none of the ten characteristics for females. Using amplified fragment length polymorphism (AFLP) DNA fingerprinting, no specific AFLP marker was detected for each type. The heterozygosity and genetic diversity were very low. Analyses of pairwise distance, the Fst index, and genetic similarity revealed similar results, with very low genetic differentiation. Therefore, there is no significant difference between blue and purple types of the crab from the West Sea of Korea, and the two types in the West Sea can be managed as one stock.

• Molecules and Cells
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• v.21 no.1
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• pp.135-140
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• 2006

Cytoplasmic male sterility (CMS) in plants, which is due to failure to produce functional pollen, is a maternally inherited trait. Specific nuclear genes that suppress CMS, termed fertility restorer (Rf) genes, have been identified in several plants. In this study, Rfl-inked molecular markers in pepper (Capsicum annuum L.) were detected by bulked segregant analysis of eight amplified fragment length polymorphisms (AFLPs). Only AFRF8 was successfully converted to a cleaved amplified polymorphic sequence (CAPS) marker. This was named AFRF8CAPS and genotype determination using it agreed with that obtained with the original AFRF8. A linkage map with a total size of 54.1 cM was constructed with AFRF8CAPS and the seven AFLP markers using the Kosambi function. The AFRF8CAPS marker was shown to be closest to Rf with a genetic distance of 1.8 cM. These markers will be useful for fast and reliable detection of restorer lines during $F_1$ hybrid seed production and breeding programs in pepper.

• Research in Plant Disease
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• v.21 no.1
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• pp.1-5
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• 2015

A PCR method has been developed for the pathovar-specific detection of Pseudomonas syringae pv. tagetis, which is the causal agent of bacterial leaf spots and apical chlorosis of several species within the Compositae family. One primer set, PSTF and PSTR, was designed using a genomic locus derived from an amplified fragment length polymorphism (AFLP) fragment produced a 554-bp amplicon from 4 isolates of P. syringae pv. tagetis. In DNA dot-blot analysis with the PCR product as probe, a positive signal was identified in only 4 isolates of P. syringae pv. tagetis. These results suggest that this PCR-based assay will be a useful method for the detection and identification of P. syringae pv. tagetis.

• Mycobiology
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• v.34 no.2
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• pp.45-55
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• 2006

Although Fursarium oxysporum causes diseases in economically important plant hosts, identification of F. oxysporum formae speciales has been difficult due to confusing phenotypic classification systems. To resolve these complexity, we evaluated genetic relationship of nine formae speciales of F. oxysporum with random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), and translation elongation factor-l alpha ($EF-1{\alpha}$) gene. In addition, the correlation between mycotoxin content of fusaric acid and isolates based on molecular marker data was evaluated using the modified Mantel's test. According to these result, these fusaric acid-producing strains could not identify clearly, and independent of geographic locations and host specificities. However, in the identification of F. oxysporum formae speciales, especially, AFLP analysis showed a higher discriminatory power than that of a the RAPD and $EF-1{\alpha}$ analyses, all three techniques were able to detect genetic variability among F. oxysporum formae speciales in this study.

• Proceedings of the PSK Conference
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• 2003.10b
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• pp.157.2-157.2
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• 2003

Panax ginseng is one of the most important medicinal plant in the Orient. The international trade of ginseng is increasing yearly. The disguise of Chinese and American ginseng into Korean ginseng became a problem in recent years in Korea and an abroad. Obviously, an effective method of authentication of Korean ginseng from others at a DNA level, is necessary for the healthy development of the ginseng market. In order to develop convenient and reproducible methods for the identification of Korean ginseng, amplified fragment length polymorphism (AFLP) analysis was applied within Panax species (Korean cultivatied and wild ginseng, Chinese wild ginseng, American cultivatied and wild ginseng). (omitted)

• Korean Journal of Breeding Science
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• v.41 no.4
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• pp.444-450
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• 2009

Amplified fragment length polymorphism (AFLP) marker was utilized for evaluation of genetic diversity of 60 pear germplasms. Twenty selective AFLP primer pairs generated a total of 522 polymorphic amplification products. From UPGMA (unweighted pair-group method arithmetic average) cluster analysis by using polymorphic bands, the pear germplasms were divided into four clusters by similarity index of 0.691. The first cluster (I) included European pears belonging to Pyrus communis and wild species such as P. nivalis and P. cordata. The second cluster (II) included Ussurian pea pears belonging to P. betulaefolia and P. fauriei. The third cluster (III) included pea pears belonging to P. calleryana and P. koehnei. Most of germplasms belonging to P. pyrifolia and P. ussuriensis, and interspecific hybrids were included in the fourth (IV) cluster. Therefore pear germplasms originated from East Asia were closely related to P. pyrifolia and P. ussuriensis. Similarity values among the tested pear germplasms ranged from 0.584 to 0.879, and the average similarity value was 0.686.

• 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.

• Molecules and Cells
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• v.25 no.2
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• pp.196-204
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• 2008

Despite increasing awareness of the importance of WRKY genes in plant defense signaling, the locations of these genes in the Capsicum genome have not been established. To develop WRKY-based markers, primer sequences were deduced from the conserved sequences of the DNA binding motif within the WRKY domains of tomato and pepper genes. These primers were derived from upstream and downstream parts of the conserved sequences of the three WRKY groups. Six primer combinations of each WRKY group were tested for polymorphisms between the mapping parents, C. annuum 'CM334' and C. annuum 'Chilsung-cho'. DNA fragments amplified by primer pairs deduced from WRKY Group II genes revealed high levels of polymorphism. Using 32 primer pairs to amplify upstream and downstream parts of the WRKY domain of WRKY group II genes, 60 polymorphic bands were detected. Polymorphisms were not detected with primer pairs from downstream parts of WRKY group II genes. Half of these primers were subjected to $F_2$ genotyping to construct a linkage map. Thirty of 41 markers were located evenly spaced on 20 of the 28 linkage groups, without clustering. This linkage map also consisted of 199 AFLP and 26 SSR markers. This WRKY-based marker system is a rapid and simple method for generating sequence-specific markers for plant gene families.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.49 no.4
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• pp.358-362
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• 2004

In order to develop molecular markers related to stay green phenotype, AFLP analysis was conducted using near-isogenic lines for either stay green or non stay green trait. Both lines have characteristics of multi-ear and tillers (MET). Two out of 64 primer combinations of selective amplification identified three reproducible polymorphic fragments in MET corn with stay green. Both of E+AGC/M+CAC and E+AAG/M+CAA primer combinations produced two and one specific polymorphic fragments linked to stay green trait, respectively. For the conversion of AFLPs to sequence tag sites (STSs), primers were designed form both end sequences of each two polymorphic fragments. One fragment, which was amplified with E+AAG/M+CAA primer combinations, possessed 298 bp long and showed a $91\%$ homology with maize retrotransposon Cinful-l. One out of two polymorphic fragments produced with E+AGC/M+CAC primer combination had 236 bp long and matched a $96\%$ homology with an intron region of 22kDa alpha zein gene cluster in Zea mays. One out of two PCR fragments amplified with MET2 primer set in the stay green MET was not produced in the non-stay green MET. The developed AFLP and STS marker could be used as an efficient tool for selection of the stay green trait in the MET inbred.