• Korean Journal of Plant Resources
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• v.17 no.2
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• pp.116-121
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• 2004

Panax ginseng discarded and lower than 4th grade is caused by red skin disease showing red color skin in ginseng. This kind of red skin ginseng is found a lot in Panax ginseng rather than Panax quinquefolium, and it is considered that red skin disease might be caused by gene. Therefore, this study was carried out to detect genes resistant to red skin disease using RT-PCR. RNA was extracted from three years old ginseng root of both red skin and normal portion in the same root. After RNA extraction, PCR amplification was performed from cDNA using many random primers. As a result, specific band for red skin was found. It is considered that the gene forming band has possibility to be related with red skin disease, and this gene should be decided if it's related with red skin disease. If that gene is related with red skin disease, it will be used for transformation to foster for resistance to red skin disease as well as for selection marker. Bowever, if it's not related with red skin disease, more primers should be used to find gene related with red skin disease.

• Korean Journal of Microbiology
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• v.46 no.3
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• pp.296-302
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• 2010

Microcystis (Cyanobacteria, Chroococcales) is one of the green tide-causing organisms in freshwaters, and some species produce microcystin that is hepatotoxin. In the aspects of freshwater quality controls and health concerns, therefore it is necessary to manage the harmful organisms. In the present study, RNA polymerase beta subunit (rpoB) gene sequences of Microcystis were determined and characterized in order to use a potential marker for the molecular detections of the species. Microcystis rpoB showed high divergences of DNA similarity and genetic distances when compared with those of 16S rRNA, and the molecular differences were statistically significant (Student t-test, p<0.05). Parsimony analyses showed the rpoB gene evolves more than 2-fold faster than 16S rRNA. In addition, phylogeny of the rpoB gene separated each M. aeruginosa strain more clearly compared with a 16S rRNA tree. This study found that the order Chroococcales, including Microcystis, has approximately two rRNA operons and single copy of the rpoB gene in their chromosomes. These results suggest that the rpoB gene is a useful marker for the molecular phylogenetics and the detection of Microcystis.

• Horticultural Science & Technology
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• v.30 no.5
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• pp.557-567
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• 2012

This study was conducted to achieve basal information for the development of tomato cultivars with disease resistances through marker-assisted backcross (MAB). Ten inbred lines with TYLCV, late blight, bacterial wilt, or powdery mildew resistance and four adapted inbred lines with superior horticultural traits were collected, which can be useful as the donor parents and recurrent parents in MAB, respectively. Inbred lines collected were evaluated by molecular markers and bioassay for confirming their disease resistances. To develop DNA markers for selecting recurrent parent genome (background selection) in MAB, a total of 108 simple sequence repeat (SSR) primer sets (nine per chromosome at average) were selected from the tomato reference genetic maps posted on SOL Genomics Network. Genetic similarity and relationships among the inbred lines were assessed using a total of 303 polymorphic SSR markers. Similarity coefficient ranged from 0.33 to 0.80; the highest similarity coefficient (0.80) was found between bacterial wilt-resistant donor lines '10BA333' and '10BA424', and the lowest (0.33) between a late blight resistant-wild species L3708 (S. pimpinelliforium L.) and '10BA424'. UPGMA analysis grouped the inbred lines into three clusters based on the similarity coefficient 0.58. Most of the donor lines of the same resistance were closely related, indicating the possibility that these lines were developed using a common resistance source. Parent combinations (donor parent ${\times}$ recurrent parent) showing appropriate levels of genetic distance and SSR marker polymorphism for MAB were selected based on the dendrogram. These combinations included 'TYR1' ${\times}$ 'RPL1' for TYLCV, '10BA333' or '10BA424' ${\times}$ 'RPL2' for bacterial wilt, and 'KNU12' ${\times}$ 'AV107-4' or 'RPL2' for powdery mildew. For late blight, the wild species resistant line 'L3708' was distantly related to all recurrent parental lines, and a suitable parent combination for MAB was 'L3708' ${\times}$ 'AV107-4', which showed a similarity coefficient of 0.41 and 45 polymorphic SSR markers.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.10a
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• pp.66-66
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• 2018

국화과(Compositae) 다년생 초본인 산국속(Dendranthema)은 국내 약 13여종이 자생하는 것으로 알려져 있으며, 이 중 감국(D. indicum (L.) Des Moul.)과 산국(D. boreale (Makino) Ling ex Kitam.), 구절초(D. zawadskii var. latilobum (Maxim.) Kitam.)가 주로 차 또는 한약재 등의 원료로 이용되고 있다. 차로 이용되는 꽃은 산국이 감국에 비해 상대적으로 작아서 구분이 가능하지만 시중에는 건조된 형태로 가공 유통되므로 육안으로 구분이 쉽지 않고, 산국 유래 제품들은 국내에서 감국 또는 국화로 혼용해서 표기되어 유통되고 있어 그 기원을 명확히 정립할 필요가 있다. 이에 본 연구는 감국과 산국의 분자유전학적 판별을 위해 DNA 바코드 후보 유전자를 활용하여 염기서열분석으로 확보된 SNP 및 InDel 정보를 바탕으로 CAPS 마커를 개발하고자 수행되었다. 감국과 산국 모두 trnL-trnF intergenic spacer 구간에서 약 1kb의 PCR 산물이 확인되었고, 이들 염기서열에서 분석한 2 SNP 및 3 InDel을 대상으로 CAPS 마커 개발을 위한 제한효소 사이트를 탐색하였다. Gap을 포함한 774bp (감국/산국=A/G) 위치의 SNP에서 BstUI(GC^GC)처리로 CAPS 마커로 전환 가능함이 확인되었고, 이에 감국과 산국의 PCR 산물에 제한효소를 처리한 결과, 제한효소 인식 사이트가 존재하는 산국에서 두 개의 DNA 단편이 확인되었다. 위 결과는 다양한 형태로 가공 유통되는 감국과 산국의 판별을 위한 마커로 활용될 수 있으며, 본 연구에 활용된 기술은 추후 건강기능식품 개발을 위한 원료표준화 확립 연구에 유용할 것으로 판단된다.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2022.09a
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• pp.66-66
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• 2022

속성수로 활용되는 버드나무속 식물들은 생식기관과 영양기관의 성장 시기가 달라 형태적 특성 평가를 위해 수년간의 조사 기간이 요구된다. 따라서 바이오매스 우수 버드나무속 교잡종 육성의 성공 여부를 조기 판별하기 위한 식별 기술이 필요하다. DNA 마커는 식물의 생장단계와 관련 없이 탐색할 수 있으며 환경에 영향을 받지 않는 장점이 있다. 식물의 계통 분류 시 주로 사용되는 엽록체 DNA는 유전자 염기서열의 변이가 비교적 크지 않은 장점이 있으나 대부분의 활엽수에서 모계를 통해 유전되는 특징이 있다. 하지만 종간 교잡종의 식별은 각각의 부모종과 구분할 수 있어야 하므로 본 연구는 엽록체 DNA가 아닌 핵 DNA를 대상으로 분석하였다. 본 연구의 목적은 호랑버들을 암나무로 갯버들을 수나무로 인공교배하여 육성된 종간 교잡종을 식별하는 핵 DNA 마커를 탐색하는 것이다. 이를 위해 버드나무속에서 개발된 총 35개의 nSSR (nuclear Simple Sequence Repeat) 마커를 대상으로 호랑버들과 갯버들, 종간 교잡종의 식별 가능성을 평가하였다. 분석 결과 호랑버들과 갯버들, 종간 교잡종 간 차이를 나타내는 2개의 핵 DNA 마커를 선발하였다. 따라서 선발된 핵 DNA 마커를 활용하여 호랑버들과 갯버들, 종간 교잡종의 조기 식별에 활용이 가능할 것으로 사료된다.

• Korean Journal of Plant Resources
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• v.28 no.5
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• pp.648-655
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• 2015

Balloon flower (Platycodon grandiflorum A. DC.) is a perennial plant of mainly Campanulaceae family, which have been widely used as a food ingredient and herbal medicine in East Asia. Although demands on related products and yearly cultivation area for balloon flower are increasing, diverse fundamental technologies and molecular breeding studies are not very well supported in Platycodons. In this study, 30 random amplification of polymorphic DNA (RAPD) primers were test in an attempt to explore genetic diversities. In addition, sequences information of the actin gene, a well conserved gene encoding a globular protein that forms microfilaments, was retrieved and analyzed. Two actin homologs were recovered; 3.4 kb fragment is a Pg-actin and 1.4 kb fragment is a Pg-actin homolog with 28.6% similarity. We have confirmed that the Pg-actin gene is configured into 4 exons and 3 introns. A single nucleotide polymorphism (SNP), G↔A, was detected on the intron 3, which served as a target for the CAPS marker development. The marker Pg-Actin-Int3 was applied to 32 balloon flower accessions. Balloon flower DNA sequence information generated in this study is expected to contribute to the analysis and molecular breeding and genetic diversity analysis of balloon flowers.

• Korean Journal of Breeding Science
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• v.42 no.5
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• pp.502-506
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• 2010

Soybean seed possesses about 15 allergenic proteins recognized by IgEs from soy-sensitive human. The allergenic impact of soybean proteins limit its extensive usage in a broad range of processed foods. Soybean protein P34 or Gly m Bd 30k of the cysteine protease family is one of the major allergen of the soybean seed. P34-null soybean, PI567476, was identified among soybean (Glycine max & Glycine soja Sieb. and Zucc) of approximately 16,226 accessions from USDA soybean germplasm screened. Also, for P34 gene (Williams 82; whole genome sequence cultivar) and P34 null gene (PI567476) comparative analysis of sequences listed in the NCBI database showed the presence of a SSLP (Simple Sequence Length Polymorphism) of 4 base pair. So, a SSLP marker was designed to reveal the polymorphism of the locus. In this study, a population of 339 $F_2$ recombinant inbred lines generated by cross between Taekwang (Glycine max) and PI567476 was used to select $F_{2:3}$ plant of a P34 null gene. The result separation rate Taekwang type, heterozygous type and PI567476 type were shown in 85: 187: 67 since single gene is concerned in as the separation rate of 1:2:1 in $X^2{_{0.05}}=5.99$, df=2. In future, selected plant will identify protein level, whether P34 null protein is equal to P34 null gene.

• Journal of KIISE
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• v.45 no.1
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• pp.61-68
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• 2018

The identification of genes that contribute to the prediction of prognosis in patients with cancer is one of the challenges in providing appropriate therapies. To find the prognostic genes, several classification models using gene expression data have been proposed. However, the prediction accuracy of cancer prognosis is limited due to the heterogeneity of cancer. In this paper, we integrate microarray data with biological network data using a modified PageRank algorithm to identify prognostic genes. We also predict the prognosis of patients with 6 cancer types (including breast carcinoma) using the K-Nearest Neighbor algorithm. Before we apply the modified PageRank, we separate samples by K-Means clustering to address the heterogeneity of cancer. The proposed algorithm showed better performance than traditional algorithms for prognosis. We were also able to identify cluster-specific biological processes using GO enrichment analysis.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.04a
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• pp.56-56
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• 2018

토마토에서 과형은 과실의 여러 가지 형질 중에서 눈에 가장 잘 띄는 형질이며, 소비자의 토마토를 구매를 결정하는데 많은 영향을 미치는 중요한 형질이다. 토마토의 과형을 결정하는 여러 가지 유전자 중에 OVATE는 둥근 토마토 과일을 서양 배 모양(pear shape)의 과일로 전환하는데 결정적인 역할을 하는 유전자이다. OVATE 유전자에 의해서 과일의 모양이 변하는 것은 조기종결 코돈을 초래하는 열성 돌연변이에 의해서 유도되며, 단백질의 C-말단 영역이 제거됨에 따라 그 기능을 상실하여 나타나는 현상이다. OVATE 유전자는 주로 식물의 생식기관에서 발현되며, 꽃에서는 개악하기 10일전부터부터 전사체가 만들어지고 발달중인 과실에서는 개약 후 8일까지 전사체를 확인할 수 있다. 토마토 분자육종 과정에서 과형 판별을 위해서 OVATE 유전자 연관 분자표지는 보고된 바 있으나 OVATE 유전자 유래 분자표지는 보고된바가 없다. 본 연구에서 국내에서 육성된 육종 라인들의 resequencing을 통해 OVATE 유전자 염기서열간의 SNP를 발견하고 이들을 dCAPS 마커로 전환하여 분자표지를 개발했다. 이러한 분자표지는 둥근 토마토(round)와 서양 배모양(pear shape)토마토 육종 프로그램의 효율성과 정확성을 향상시키는데 활용할 수 있을 것으로 기대한다.

• Microbiology and Biotechnology Letters
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• v.33 no.4
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• pp.241-247
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• 2005

A new lactococcal shuttle/expression vector for lactococci, pWgal13T, was constructed using a $\beta$-galactosi-dase gene (lacZ) from Lacfococcus lactis ssp. lactis ATCC 7962 as a screening marker. The pWgal 13T was introduced into Escherichia coli DH5a and L. lactis MG1363, and was easily detected by the formation of blue colonies on a medium containing X-gal without any false transformants. Also, the quantitatively lacZ activity of pWgal13T was measured in L. lactis ssp. cremoris MG1363, and was found to be four times higher than that of L. lactis ssp. lactis ATCC7962 grown on a medium containing glucose, which shows that the lacZ gene of pWgal13T can be used for the efficient screening of L. lactis on general media. The pWgal13T was equipped with a lactococcal replicon of pWV01 from L. lactis Wg2, the new promoter P13C from L. lactis ssp. cremoris LM0230, multiple cloning sites, and a terminator for the expression of a relevant gene. The vee-tor pWgal13T was used for the expression of the EGFP gene in E. coli and L. lactis. These results show that the lactococcal expression/shuttle vector constructed in the present study can be used for the production of foreign proteins in E. coli and L. lactis.