• Journal of Korean Society of Forest Science
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• v.96 no.2
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• pp.125-130
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• 2007

The principal morphological characters used for identification of hydrangea cultivars are often dependent on agroclimatic conditions. Furthermore, information on the selection or the genetic background of the hydrangea breeding is so rare that a molecular marker system for cultivar identification is needed. Amplified fragment length polymorphism (AFLP) markers were employed for fingerprinting Hydrangea macrophylla cultivars and candidate cultivars of H. macrophylla selected in Korea. One AFLP primer combination was sufficient to distinguish 17 H. macrophylla cultivars and 4 candidate cultivars. The profile of 19 loci that can minimize the error of amplification peak detection was constructed. AFLP markers were efficient for identification, estimation of genetic distances between cultivars, and cultivar discrimination. Based on the observed AFLP markers, genetic relationship was reconstructed by the UPGMA method. Seventeen H. macrophylla cultivars and H. macrophylla for. normalis formed a major cluster, and candidate cultivars selected in Korea formed another cluster.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.8
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• pp.1106-1110
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• 2006

In the meat industry, correct breed information in food labeling is required to assure meat quality. Genetic markers provide corroborating evidence to identify breed. This paper describes the development of DNA markers to discriminate between Japanese Black and F1 (Japanese Black${\times}$Holstein) breeds. The amplified fragment length polymorphism method was employed to detect candidate markers absent in Japanese Black but present in Holstein. The 1,754 primer combinations yielded eleven markers that were converted into single nucleotide polymorphism markers for high-throughput genotyping. The allele frequencies in both breeds were investigated for discrimination ability using PCR-RFLP. The probability of identifying F1 was 0.9168 and probability of misjudgment was 0.0066 using four selected markers. The markers could be useful for discriminating between Japanese Black and F1 and would contribute to the prevention of falsified breed labeling of meat.

• The Korean Journal of Physiology and Pharmacology
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• v.14 no.5
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• pp.265-272
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• 2010

Follicular cystic ovary (FCO) is one of the most frequently diagnosed ovarian diseases and is a major cause of reproductive failure in mammalian species. However, the mechanism by which FCO is induced remains unclear. Genetic alterations which affect the functioning of many kinds of cells and/or tissues could be present in cystic ovaries. In this study, we performed a comparison analysis of gene expression in order to identify new molecules useful in discrimination of bovine FCO with follicular cystic follicles (FCFs). Normal follicles and FCFs were classified based on their sizes (5 to 10 mm and $\geq25mm$). These follicles had granulosa cell layer and theca interna and the hormone $17{\beta}$-estradiol ($E_2$)/ progesterone ($P_4$) ratio in follicles was greater than one. Perifollicular regions including follicles were used for the preparation of RNA or protein. Differentially expressed genes (DEG) that showed greater than a 2-fold change in expression were screened by the annealing control primer (ACP)-based PCR method using $GeneFishing^{TM}$ DEG kits in bovine normal follicles and FCFs. We identified two DEGs in the FCFs: ribosomal protein L15 (RPL15) and microtubule-associated protein 1B (MAP1B) based on BLAST searches of the NCBI GenBank. Consistent with the ACP analysis, semi-quantitative PCR data and Western blot analyses revealed an up-regulation of RPL15 and a down-regulation of MAP1B in FCFs. These results suggest that RPL15 and MAP1B may be involved in the regulation of pathological processes in bovine FCOs and may help to establish a bovine gene data-base for the discrimination of FCOs from normal ovaries.

• BMB Reports
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• v.31 no.6
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• pp.525-535
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• 1998

A critical step in the faithful translation of genetic information is specific tRNA recognition by aminoacyl-tRNA synthetases. These enzymes catalyze the covalent attachment of particular amino acids to the terminal adenosine of cognate tRNA substrates. In general, there is one synthetase for each of the twenty amino acids and each enzyme must discriminate against all of the cellular tRNAs that are specific for the nineteen noncognate amino acids. Primary sequence information combined with structural data have resulted in the division of the twenty synthetases into two classes. In recent years, several high-resolution co-crystal structures along with biochemical data have led to an increased understanding of tRNA recognition by synthetases of both classes. The anticodon sequence and the amino acid acceptor stem are the most common locations for critical recognition elements. This review will focus on acceptor stem discrimination by class II synthetases. In particular, the results of in vitro aminoacylation assays and site-directed and atomic group mutagenesis studies will be discussed. These studies have revealed that even subtle atomic determinants can provide signals for specific tRNA aminoacylation.

• Journal of Plant Biotechnology
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• v.34 no.3
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• pp.201-205
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• 2007

To determine whether pattern recognition based on metabolite fingerprinting for whole cell extracts of higher plants is applied to discriminate plants genetically, leaf samples of eight cultivars of Catharanthus roseus were subjected to Fourier transform infrared spectroscopy (FT-IR). FT-IR fingerprint region data were analyzed by principal component analysis (PCA). Major peaks as biomarkers were identified as the most significant contributors to distinguish samples by using genetic programming. A hierarchical dendrogram based on the results from PCA separated the eight cultivars into two major groups in the same manner as the dendrograms based on genetic fingerprinting methods such as RAPD and AFLP. A slight difference between the dendrograms was found only in branching pattern within each subgroup. Therefore, we conclude that the hierarchical dendrogram based on PCA of the FT-IR data represents the most probable chemotaxonomical relationship between cultivars, which is in general agreement with the genetic relationship determined by conventional DNA fingerprinting methods.

• Horticultural Science & Technology
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• v.30 no.3
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• pp.278-285
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• 2012

Cymbidium goeringii is one of the most important and popular species in the orchid family in north-east Asia. In the present study, we prepared multiplex PCR system, and used it for the genotyping of eight simple sequence repeats (SSR) markers (CG409, CG415, CG709, CG722, CG787, CG1023, CG1210, and CG1281) in subject with 40 samples of cultivated varieties. All the analyzed samples showed different combined genotypes. The average combined power of discrimination was very high value of $7.14{\times}10^{-10}$, and observed heterozygosity (Ho = 0.466) was similar with two wild populations of C. goeringii, which may indicate no or little occurrence of genetic change after collection from wild habitats. The present study also developed a two-dimensional barcode to express information of genotype results of eight SSR markers (SSR DNA ID). The discrimination power of DNA ID between two individuals will be statistically more than 99.999999%. The SSR DNA ID and two-dimensional barcode may be very usefully applied for the discrimination and maintence of cultivars of C. goeringii.

• Animal Systematics, Evolution and Diversity
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• v.26 no.1
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• pp.15-19
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• 2010

The Russian ratsnake, Elaphe schrenckii, is found in Russia, China, and Korea, and is considered to be an endangered species by the Ministry of Environment in South Korea. Due to habitat loss and use in oriental medicine, their population has been severely decimated. In South Korea, two subspecies of E. schrenckii has been defined according to body color: E. s. schrenckii (blackish) and E. s. anomala (yellow-brownish). Molecular genetic studies on Elaphe schrenckii are very scarce and the taxonomy of Elaphe schrenckii subspecies is uncertain. From the present study, we attempted to identify the genetic differences of these two subspecies using species-specific microsatellites developed from the genomic library of E. schrenckii. Nine polymorphic loci were tested on 19 individuals from E. s. schrenckii (n=10) and E. s. anomala (n=9) in South Korea. The mean number of alleles was 3.78 in E. s. schrenckii and 4.11 in E. s. anomala. The average expected heterozygosity was 0.542 and 0.511 in E. s. schrenckii and E. s. anomala, respectively. We found a lack of genetic structure between two subspecies ($F_{ST}=0.016$) and no genetic discrimination between two subspecies was found. Based on the present findings by microsatellites, two subspecies can be considered as one species, E. schrenckii. However, further investigations on taxonomical status using mitochondrial and nuclear DNA sequences need to be performed and morphological & ecological data should be revised. The genetic markers should benefit future studies of the endangered species of other Elaphe species for the study of genetic diversity and potential conservation management.

• Journal of Ginseng Research
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• v.34 no.1
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• pp.41-46
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• 2010

Expensive herbs such as ginseng are always a possible target for fraudulent labeling. New mountain ginseng strains have occasionally been found deep within mountain areas and commercially traded at exorbitant prices. However, until now, no scientific basis has existed to distinguish such ginseng from commonly cultivated ginseng species other than by virtue of being found within deep mountain areas. Polymerase chain reaction (PCR) analysis of the internal transcribed spacer has been shown to be an appropriate method for the identification of the most popular species (Panax ginseng) in the Panax ginseng genus. A single nucleotide polymorphism (SNP) has been identified between three newly found mountain ginseng (KGD4, KGD5, and KW1) and already established Panax species. Specific PCR primers were designed from this SNP site within the sequence data and used to detect the mountain ginseng strains via multiplex PCR. The established multiplex-PCR method for the simultaneous detection of newly found mountain ginseng strains, Korean ginseng, and foreign ginseng in a single reaction was determined to be effective. This study is the first report of scientific discrimination of "mountain ginsengs" and describes an effective method of identification for fraud prevention and for uncovering the possible presence of other, cheaper ginseng species on the market.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.46 no.2
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• pp.112-120
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• 2001

Genetic diversity of 47 East-Asian vegetable soybean was characterized by means of agro-morphological traits and RAPD markers. A field trial was conducted to evaluate 14 agro-morphological traits. To study RAPD-based DNA analysis, a total of sixty 10-mer random primers were screened. Of these, 23 polymorphic markers in 16 varieties used for screening. Among 207 markers amplified, 48 were polymorphic for at least one pairwise comparison within the 47 varieties. A higher differentiation level between varieties was observed by using RAPD markers compared to morphological markers. Correspondence analysis using both types of marker showed that RAPD data could fully discriminate between all varieties, whereas morphological markers could not achieve a complete discrimination. Genetic distances between the varieties were estimated from simple matching coefficients, ranged from 0.0 to 0.640 with an average of 0.295$\pm$0.131 for morphological traits and 0.042 to 0.625 with an average of 0.336$\pm$0.099 for RAPD data, respectively. Cluster analysis based on genetic dissimilarity of these varieties gave rise to 4 distinct groups. The clustering results based on RAPDs did not match with those based on morphological traits. Geographical distribution of most varieties in each of the groups were not well defined. The results suggested that the level of genetic diversity within this group of East-Asian vegetable soybean varieties was sufficient for a breeding program and can be used to establish genetic relationships among them with unknown or unrelated pedigrees.

• The Korean Journal of Malacology
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• v.24 no.1
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• pp.11-24
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• 2008

GDNA was isolated from the jedo venus clam (Protothaca jedoensis, Lischke) from Boryeong (jedo venus clam from Boryeong JVCB) and Wonsan (jedo venus clam from Wonsan; JVCW) located in the West Sea and the East Sea of Korean Peninsula, respectively and we performed clustering analyses, DNA polymorphisms and the populations genetic variations. In the present study, the seven decamer primer generated the one hundred and eleven major/minor specific bands in JVCB population and ninety four-specific bands in JVCW population. Seven primers generated the unique shared bands to each population of one hundred and seventy-six, on average of 25,1, in JVCB population from Boryeong and three hundred thirty, on average of 47,1, in JVCW population from Wonsan, respectively. The dendrogram obtained by the seven oligonucleotides primers, indicates two genetic clusters. Especially, two Protothaca between the individual WONSAN no. 12 and BORYEONG no. 10 showed the longest genetic distance (0.537) in comparison with other individuals used. Accordingly, RAPD analysis showed that the JVCB was a little more genetically diverse than the JVCW population. This result implies the genetic similarity owing to rearing in the same and/or similar circumstances or inbreeding within the JVCW population. So to speak, JVCB population may have high levels of genomic DNA variability owing to the introduction of the wild individuals from the other sites to sampling sites although it may be the geographically diverse distribution of this species. However, it was confirmed that it did not appear like that really in this study. We feel convinced that RAPD analysis discovered a significant genetic distance between two Protothaca population pairs (P<0.001). The existence of population discrimination and genetic diversity between two Protothaca populations was identified by RAPD analysis.