• Biomedical Science Letters
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• v.29 no.4
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• pp.302-313
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• 2023

Y chromosomal short tandem repeat (Y-STR) markers have been developed continuously to complement forensic DNA analyses and population genetic studies. Initially, we collected data from previously reported Korean population Y-STR haplotype studies on 1133 individuals. We then conducted a marker expansion analysis using a dataset from the Y-STR Haplotype Reference Database (YHRD), covering up to 29 Y-STRs, referred to as Ymax. Additionally, we examined the impact of rapidly mutating (RM) Y-STRs included in this expanded marker set on the discrimination capacity. We observed that marker expansions both with (0.9896), and without (0.9510), RM Y-STR improved the discrimination capacity. Subsequently, we focused on 16 individuals belonging to seven distinct groups sharing identical haplotypes. These particular haplotypes had been previously identified among 476 unrelated males using 23 Y-STR markers from the PowerPlex^® Y23 System. We expanded the marker panel up to Ymax to explore how discrimination improved with an expansion of Y-STR markers for these 16 individuals. Among the expanded markers, DYS627, which had high discriminatory power, had a high mutation rate (1.10 × 10^-2) and high gene diversity (0.83). In contrast, DYF387S1 displayed high gene diversity (0.95) but a relatively low mutation rate (2.80 × 10^-3). We propose that these findings will be valuable in the selection of suitable Y-STR markers, depending on the objectives of forensic analyses. Additionally, the presence of frequently observed Y-haplotypes in Korean population will facilitate statistical interpretation in Y-STR DNA profiling.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.28 no.8C
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• pp.803-810
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• 2003

This paper addresses an image processing technique for the human papillomavirus (HPV) DNA chip to discriminate whether the probes are hybridized with the target DNA. HPV DNA chip is designed to determine HPV gene-types by using DNA probes for 22 HPV types. In addition to the probes, the HPV DNA chip has markers that always react with the sample DNA. The positions of probe-dots in the final scanned image are fixed relative to the marker- dot locations with a small variation attributable to the accuracy of the dotter and the scanner. The probes are quadruplicated to enhance diagnostic fidelity. frier knowledge including the marker relative distance and the replication information of probes is integrated into the template matching technique with normalized covariance measure. It was demonstrated that the employment of both of the prior knowledges can be accomplished by simply averaging the template matching measures over the positions of the markers and probes. The resulting proposed scheme yields stable marker locating and probe classification.

• Journal of Life Science
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• v.21 no.3
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• pp.385-392
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• 2011

The otter (Lutra lutra) in Korea is classified as a first grade endangered species and is managed under state control. We performed a phylogenetic analysis of the otter that inhabits the Changnyeong, Jinju, and Geoje areas in Gyeongsangnamdo, Korea using mtDNA and microsatellite (MS) markers. As a result of the analysis using the 676-bp D-loop sequence of mtDNA, six haplotypes were estimated from five single nucleotide polymorphisms. The genetic distance between the Jinju and Geoje areas was greater than distances within the areas, and the distance between Jinju and Geoje was especially clear. From the phylogenetic tree estimated using the Bayesian Markov chain Monte Carlo analysis by the MrBays program, two subgroups, one containing samples from Jinju and the other containing samples from the Changnyeong and Geoje areas were clearly identified. The result of a parsimonious median-joining network analysis also showed two clear subgroups, supporting the result of the phylogenetic analysis. On the other hand, in the consensus tree estimated using the genetic distances estimated from the genotypes of 13 MS markers, there were clear two subgroups, one containing samples from the Jinju, Geoje and Changnyeong areas and the other containing samples from only the Jinju area. The samples were not identically classified into each subgroup defined by mtDNA and MS markers. It could be inferred that the differential classification of samples by the two different marker systems was because of the different characteristics of the marker systems used, that is, the mtDNA was for detecting maternal lineage and the MS markers were for estimating autosomal genetic distances. Nonetheless, the results from the two marker systems showed that there has been a progressive genetic fixation according to the habitats of the otters. Further analyses using not only newly developed MS markers that will possess more analytical power but also the whole mtDNA are needed. Expansion of the phylogenetic analysis using otter samples collected from the major habitats in Korea should be helpful in scientifically and efficiently maintaining and preserving them.

• Fisheries and Aquatic Sciences
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• v.9 no.3
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• pp.101-106
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• 2006

The cytochrome c oxidase subunit I (COI) gene region of mitochondrial DNA (mtDNA) was examined in four abalone species to estimate its utility as a genetic marker using restriction fragment length polymorphism (RFLP) analysis. The utility was evaluated in terms of genetic divergence and relationships among Haliotis discus hannai, H. rufescens, H. rubra, and H. midae in both hemispheres of the world. There was clear genetic divergence in the mtDNA COI region between all pairs of the four species. Moreover, relationships among the abalone species were reflected in their geographical distributions and morphological characteristics. Therefore, RFLP analysis of the mtDNA COI region is a suitable genetic marker for the estimation of genetic divergence and relationships among abalone species. However, it is not effective for the evaluation of genetic differences within abalone species.

• Korean Journal Plant Pathology
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• v.12 no.1
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• pp.41-46
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• 1996

본 실험은 이병 딸기의 조직에서 분리 동정된 시들음병균(Fusarium oxysporum f. sp. fragariae) 균주들의 유？거 변이를 random amplified polymorphic DNA(RAPD) marker들을 이용하여 조사하였다. 총 24개의 딸기 시들음병 균주들의 DNA를 주형으로 하여 16개의 random 10-mer primer들을 사용하여 증폭시킨 결과 총 231개의 marker들을 이용하여 유전적 변이를 조사해 본 결과 크게 RAPD I과 RAPD II의 2개 그룹으로 나눌 수 있었다. RAPD I그룹에 속하는 균주는 VCG A에 속하는 Y1, K1, K2, K3, K4, N2, N3, N4-1, N6-1, N6-2, N8, N9, N10, M1-2-1 균주, VCG B에 속하는 M4-1 균주 그리고 VCG C에 속하는 N1, Y2 균주들이었고, RAPD II그룹에는 VCG B에 속하는 M1-1, M2-2-1, M2-4-2, M3-2, M3-3-2 균주와 VCG D에 속하는 N1 1 균주가 속하였다. 이들 2그룹 간에는 31%의 유사성이 있었다.

• Proceedings of the Zoological Society Korea Conference
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• 2001.10a
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• pp.120.2-120
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• 2001

• Development and Reproduction
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• v.15 no.4
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• pp.315-324
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• 2011

This study was conducted to detect the specific expressing genes by using RAPD-PCR and RFLP method in the Korea Native Brindled Cattle, Korean Native cow and Holstein cattle. And then, the specific marker gene was investigated by the analysis of the genes for detection significance according to the expressing pattern. We found the specific expression gene by the RAPD-PCR analysis in Korea Native Brindled Cattle. It was detected the differences of the species in the colour and external section. The Korea Native Brindled Cattle were vary low compare to the Korean Native cow and Holstein cattle by analysis result of polymorphism and distribution. And there were a found the specific marker gene by sequencing in the R9B gene fragment of Korea Native Brindled Cattle. And the sequencing result of the R9B was different between Korean Native cow and Holstein cattle. Thus, this gene can be apply as the specific marker gene in the Korea Native Brindled Cattle.

• 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.

• Journal of Life Science
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• v.11 no.1
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• pp.65-67
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• 2001

In order to develop a rapid and simple method for testing the purity of radish hybrid seeds using a procedure based on the PCR(Polymerase chain reaction), eighty random primers were screened with the genomic DNA extracted from five day old seedlings of inbred parent lines and their F1 hybrids. Two primers, HRM-02 (5'-GAGACCAGAC-3') and HRM-19(5'-TGAGGCGTGT-3'), generate reproducible unique PCR patterns which can identify each parent lines as well as their hybrids. In actual test of randomly selected hybrid seeds using the two marker primers, the purity tested by one primer was exactly same as that of other primer. It suggests that one marker primer selected in this experiment is enough for the purity test of radish hybrid seeds. We demonstrates the use of RAPD(randomly amplified polymorphic DNAs) markers to identify each of inbred parent lines and hybrids by rapid and simple method.

• Plant Resources
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• v.7 no.2
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• pp.136-140
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• 2004

Co-segregation of male fertility with DNA markers selected by RAPD analysis as being potentially linked to the restorer gene (Rf) for Cytoplasmic male sterility (CMS) was analyzed using segregating F2 population. One RAPD marker directly linked to the Rf locus was identified. Amplification of OPT-02/570 using the STS primers generated a monomorphic band of each fertile plants randomly selected F2 progenies. From these results, this specific marker would be strongly linked to be restoring gene. The use of STS marker is effective in overcoming the reliability of the RAPD phenotype and improving their utility for MAS, co-dominant STS markers are especially very useful.