• Fisheries and Aquatic Sciences
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• 제11권1호
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• pp.36-40
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• 2008

We analyzed the nucleotide sequences of about 500 bp of the mitochondrial NADH dehydrogenase subunit 3 (ND3) gene to estimate the genetic variation of Korean masu salmon (Oncorhynchus masou) populations. DNA samples were collected from 104 river-only specimens and 52 anadromous specimens from three hatcheries and one river. There are no records of artificial release into the river. We amplified the ND3 gene by polymerase chain reaction, targeting areas that included parts of the cytochrome oxidase III gene and the NADH dehydrogenase subunit 4L gene, and defined 14 haplotypes based on 12 variable nucleotide sites in the examined region. Among the haplotypes, ten were specific to river-only specimens within hatchery populations. Haplotype diversity of river-only populations in hatcheries was higher than that of anadromous and wild populations. Pairwise population $F_{ST}$ estimates and neighbor-joining tree analyses inferred that anadromous and river-only populations were distinct. These results suggest that sequence polymorphism in the ND3 region may be a useful marker for analyzing the genetic variation and population structure of masu salmon.

• Plant Resources
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• 제3권3호
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• pp.211-218
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• 2000

Intraspecific genetic relationship of 19 variation types of the Yam (Dioscorea alata) classified by their external morphological characteristics such as leaf and tuber shape were assessed by DNA using random and specific primer. Twenty two out of 113 primers (100 random[10-mer] primers, two 15 mer [M13 core sequence, and (GGAT)$_4$ sequence]) had been used in PCR-amplification. Only 12 primers, however, were success in DNA amplification in all of the analyzed plants, resulting in 93 randomly and specifically amplified DNA fragments. The analyzed taxa showed very high polymorphisms(69 bands, 71.0 %), allowing individual taxon to be identified based on DNA fingerprinting. Monomorphic bands among total amplified DNA bands of each primer was low under the 50%. Similarity indices between accessions were computed from PCR(polymerase chain reaction) data, and genetic relationships among intraspecific variations were closely related at the levels ranging from 0.66 to 0.90. These DNA data were not matched well with those of morphological characters since they were divided into two major groups at the similarity coefficient value of 0.70. Therefore, Grouping of species into variation types by mainly morphological charactistics was suggested unreasonable.

• 대한의생명과학회지
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• 제14권3호
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• pp.131-137
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• 2008

Adipogenesis is a complex sequence of events that culminates in the differentiation of fibroblast-like preadipocytes into specialized lipid-filled adipocytes and also involves a cascade of expression of many transcription factors such as peroxisome proliferator-activated receptor ${\gamma}(PPAR{\gamma})$ and CCAAT/enhancer-binding proteins (C/EBPs). $PPAR{\gamma}$ and C/EBPs transcriptionally transactivate adipocyte specific genes, including fatty acid transport protein (FAT/CD36) and leptin. To determine whether $17{\beta}$-estradiol modulates $C/EBP{\alpha}$ actions on adipogenesis in high fat diet-fed female ovariectomized (OVX) C57BL/6 mice, mice were treated with $17{\beta}$-estradiol for 7 days and the effects of $17{\beta}$-estradiol on adipose tissue mass and expression of adipocyte specific gene as well as $C/EBP{\alpha}$ were measured. Compared to vehicle-treated OVX control mice, OVX mice treated with $17{\beta}$-estradiol for 7 days had lower adipose tissue weights that were similar to weights in high fat diet-fed sham-operated (Sham) mice. OVX mice showed the increased expression of $C/EBP{\alpha}$ mRNA compared with Sham mice. However, $17{\beta}$-estradiol treatment in OVX mice inhibited OVX induced-$C/EBP{\alpha}$ activation, indicating that $17{\beta}$-estradiol may act as an inhibitor of $C/EBP{\alpha}$ action. Moreover, $17{\beta}$-estradiol decreased mRNA levels of adipocyte marker genes, such as lipoprotein lipase, FAT/CD36 and leptin, to levels in Sham mice. These results suggest that down-regulation of adipogenesis by $17{\beta}$-estradiol may be due to reduced adipose $C/EBP{\alpha}$ activities in female OVX C57BL/6 mice.

• Mycobiology
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• 제48권4호
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• pp.313-320
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• 2020

In Pleurotus sp., green mold, which is considered a major epidemic, is caused by several Trichoderma species. To develop a rapid molecular marker specific for Trichoderma spp. that potentially cause green mold, eleven Trichoderma species were collected from mushroom farms and the Korean Agricultural Culture Collection (KACC). A dominant fungal isolate from a green mold-infected substrate was identified as Trichoderma pleuroticola based on the sequences of its internal transcribed spacer (ITS) and translation elongation factor 1-α (tef1) genes. In artificial inoculation tests, all Trichoderma spp., including T. atroviride, T. cf. virens, T. citrinoviride, T. harzianum, T. koningii, T. longibrachiatum, T. pleurotum, and T. pleuroticola, showed pathogenicity to some extent, and the observed symptoms were soaked mycelia with a red-brown pigment and retarded mycelium regeneration. A molecular marker was developed for the rapid detection of wide range of Trichoderma spp. based on the DNA sequence alignment of the ITS1 and ITS2 regions of Trichoderma spp. The developed primer set detected only Trichoderma spp., and no cross reactivity with edible mushrooms was observed. The detection limits for the PCR assay of T. harzianum (KACC40558), T. pleurotum (KACC44537), and T. pleuroticola (CAF-TP3) were found to be 500, 50, and 5 fg, respectively, and the detection limit for the pathogen-to-host ratio was approximately 1:10,000 (wt/wt).

• Molecules and Cells
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• 제39권2호
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• pp.141-148
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• 2016

Oriental melon (Cucumis melo L. var. makuwa) is one of six subspecies of melon and is cultivated widely in East Asia, including China, Japan, and Korea. Although oriental melon is economically valuable in Asia and is genetically distinct from other subspecies, few reports of genome-scale research on oriental melon have been published. We generated 30.5 and 36.8 Gb of raw RNA sequence data from the female and male flowers, leaves, roots, and fruit of two oriental melon varieties, Korean landrace (KM) and Breeding line of NongWoo Bio Co. (NW), respectively. From the raw reads, 64,998 transcripts from KM and 100,234 transcripts from NW were de novo assembled. The assembled transcripts were used to identify molecular markers (e.g., single-nucleotide polymorphisms and simple sequence repeats), detect tissue-specific expressed genes, and construct a genetic linkage map. In total, 234 single-nucleotide polymorphisms and 25 simple sequence repeats were screened from 7,871 and 8,052 candidates, respectively, between the KM and NW varieties and used for construction of a genetic map with 94 F2 population specimens. The genetic linkage map consisted of 12 linkage groups, and 248 markers were assigned. These transcriptome and molecular marker data provide information useful for molecular breeding of oriental melon and further comparative studies of the Cucurbitaceae family.

• 생명과학회지
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• 제19권4호
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• pp.467-471
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• 2009

돼지 6품종(Landrace, Duroc, Large White, 한국재래돼지, Berkshire, Hampshire)을 대상으로 기존에 보고된 서열을 바탕으로 제작한 primer를 이용하여 mtDNA D-loop 전체영역을 증폭하였다. 증폭된 PCR product를 cloning 및 DNA sequencing, 다중염기서열비교를 통하여 분석한 결과, mtDNA에서 heteroplasmy가 나타나는 D-loop 내 tandem repeat region 이후에 11-bp 중복이 존재하는 것을 확인하였다. 이런 중복현상은 일본재래돼지와 Duroc에서 보고되었지만, 이를 이용한 돼지 품종별 중복현상의 빈도 및 분포에 관한 연구는 이루어져있지 않다. 품종별 11-bp 중복현상을 분석하기 위해서 6품종을 대상으로 중복지역을 포함한 약 150 bp 절편을 증폭하였으며, PAGE 방법을 통하여 분석하였다. 그 결과 본 연구에서 사용한 품종들 중 모든 Large White에서 중복현상이 발생하는 것을 확인하였으며, Duroc인 경우 11.2% (9/80)에서 중복현상이 확인되었다. 반면에 Landrace, 한국재래돼지, Berkshire 및 Hampshire에서는 전혀 발견되지 않았다. 이런 결과로서, 11-bp 중복현상의 분석은 현재 구별이 불가능한 Landrace와 Large White를 구별할 수 있는 유용한 DNA marker로서 사용이 가능할 것이다.

• 생명과학회지
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• 제26권7호
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• pp.855-867
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• 2016

말은 인류에 의해 상대적으로 일찍 가축화된 종 중 하나로써, 경주능력, 강건성 및 항병성 등과 같은 능력을 위해 인공적으로 선택되었다. 그 결과, 현재 경주마로 많이 쓰이고 있는 서러브레드의 게놈은 운동 능력에 특화된 유전자형을 많이 갖고 있다. 최근 NGS 기술의 도래와 함께 전장게놈을 대상으로 경주마의 우수한 유전형질을 찾는 연구가 유전체학의 관점에서 진행되고 있다. 그 결과 말의 게놈에 대해서도 GWAS (Genome-wide Association study)가 적용되고 있고, 우수 경주능력을 나타내는 유전자 마커가 발굴되고 있다. 아울러, 특정 샘플의 전장 전사체를 NGS 기법으로 분석할 수 있는 RNA-Seq 기법 역시 활용되고 있는데, 이를 통하여 각 개체별, 운동 전후, 한 개체의 조직별 특정 유전자의 발현 양상과 함께 전사체의 서열 등을 확인할 수 있다. DNA 서열의 변화 없이 유전자 발현을 조절하는 강력한 인자로써 DNA methylation이 주목받고 있다. 말의 게놈에 있어서도 운동 특이적 또는 개체 특이적 DNA methylation 패턴을 보여 주었고, 이는 우수 개체 선정을 위한 마커 개발에 좋은 단서를 제공해 줄 것이다. 유전자 발현을 억제하는 miRNA와, 포유동물의 유전체 내 절반 정도를 차지하고 있는 이동성 유전인자는 기능유전체 연구에 있어서 중요한 인자들이다. 이들은 인간의 게놈에서 많이 연구가 되어 왔으나, 말에서의 연구는 현재 미미한 실정이다. 하지만, 현재까지 말에서 되어 있는 위의 두 인자에 대한 연구 현황을 알아보고, 차후 우수 마 선별 연구에 적용될 가능성을 제시하였다. 기능유전체 및 후성유전체 분석 기법이 발전함에 따라 말에서도 본 연구에서 소개된 여러 가지 분석 기법이 적용되고, 우수한 경주마를 선정하는 데 많은 도움을 줄 것으로 기대하고 있다. 이에 현재까지의 우수한 경주마를 선택하기 위한 많은 연구들 및, 말 연구에 대한 앞으로의 발전 가능성에 대해 고찰하고 토의하였다.

• Plant Breeding and Biotechnology
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• 제6권4호
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• pp.391-403
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• 2018

Genome resequencing by next-generation sequencing technology can reveal numerous single nucleotide polymorphisms (SNPs) within a closely-related cultivar group, which would enable the development of sufficient SNP markers for mapping and the identification of useful genes present in the cultivar group. We analyzed genome sequence data from 13 Korean japonica rice varieties and discovered 740,566 SNPs. The SNPs were distributed at 100-kbp intervals throughout the rice genome, although the SNP density was uneven among the chromosomes. Of the 740,566 SNPs, 1,014 SNP sites were selected on the basis of polymorphism information content (PIC) value higher than 0.4 per 200-kbp interval, and 506 of these SNPs were converted to Kompetitive Allele-Specific PCR (KASP) markers. The 506 KASP markers were tested for genotyping with the 13 sequenced Korean japonica rice varieties, and polymorphisms were detected in 400 KASP markers (79.1%) which would be suitable for genetic analysis and molecular breeding. Additionally, a genetic map comprising 205 KASP markers was successfully constructed with 188 $F_2$ progenies derived from a cross between the varieties, Junam and Nampyeong. In a phylogenetic analysis with 81 KASP markers, 13 Korean japonica varieties showed close genetic relationships and were divided into three groups. More KASP markers are being developed and these markers will be utilized in gene mapping, quantitative trait locus (QTL) analysis, marker-assisted selection and other strategies relevant to crop improvement.

• 대한본초학회지
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• 제24권3호
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• pp.59-68
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• 2009

Objectives : Bupleuri Radix (Siho) is prescribed as the root of different Bupleurum species on the pharmarcopoeia in Korea and China. Moreover, other species and varieties of the genus Bupleurum have been also distributed on the herbal market as Bupleuri Radix. However, due to the morphological similarity and frequent occurrence of intermediate forms, the correct identification of this radix is very difficult. To develop a reliable method for correct identification and improving the quality standards of official Bupleuri Radix, we analyzed sequences of the ribosomal RNA gene and internal transcribed spacer (rDNA-ITS) region. Methods : PCR amplification of rDNA-ITS region was performed using ITS1 and ITS4 primer from 6 Bupleurum species and 1 variety, B. falcatum L. (Siho), an improved breed of B. falcatum L. (Samdo-Siho), B. chinense DC. (Buk-Siho), B. scorzonerifolium Willd. (Nam-Siho), B. longiadiatum Turcz. (Gae-Siho), B. euphorbiodes Nakai (Deungdae-Siho) and B. latissimum Nakai (Seom-Siho), and nucleotide sequence was determined after sub-cloning into the pGEM-Teasy vector. Authentic marker nucleotides were estimated by the analysis of ClastalW using entire rDNA-ITS sequence of three samples per species. Results : In comparative analysis of the rDNA-ITS sequences, we found specific nucleotides to distinguish Korean (B. falcatum L. and its variety) and Chinese official species (B. chinense DC. and B. scorzonerifolium Willd.) from others at positions 411 and 447, and positions 89, 101, 415 and 599, respectively. Futhermore, we also found nucleotide indels (insertion and/or deletion) and substitutions to identify each of different Bupleurum species, 2 positions for B. falcatum L. and its variety, 6 positions for B. chinense DC., 49 positions for B. scorzonerifolium Willd., 8 positions for B. euphorbioides Nakai, 7 positions for B. longiradiatum Nakai and 9 positions for B. latissimum Nakai. These sequence differences at corresponding positions are avaliable nucleotide markers to determine the botanical origins of Bupleuri Radix. Moreover, we confirmed the phylogenetic relationship of B. latissimum Nakai, a Korean endemic speices, among Bupleurum species based on the rDNA-ITS sequence. Conclusions : These marker nucleotides would be useful to identify the official herbal medicines by the providing of definitive information that can identify each plant species and distinguish it from unauthentic adulterant Bupleurum species.

• Genomics & Informatics
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• 제5권4호
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• pp.152-160
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• 2007

Most common diseases are caused by multiple genetic and environmental factors. Among the genetic factors, single nucleotide polymorphisms (SNPs) are common DNA sequence variations in individuals and can serve as important genetic markers. Recently, investigations of gene-based and whole genome-based SNPs have been applied to association studies for marker discovery. However, SNPs are so population-specific that the association needs to be verified. Fifty-five genes and 384 SNPs were selected based on association with disease. Genotypes of 337 SNPs in candidate genes were determined using Illumina Sentrix Array Matrix (SAM) chips by an allele-specific extension method in 364 unrelated Korean individuals. Allelic frequencies of SNPs were compared with those of other populations obtained from the International HapMap database. Minor allele frequencies, linkage disequilibrium blocks, tagSNPs, and haplotypes of functional candidate SNPs in 55 genetic disease-associated genes were provided. Our data may provide useful information for the selection of genetic markers for gene-based genetic disease-association studies of the Korean population.