• 제목/요약/키워드: DNA fingerprinting

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DNA Fingerprinting of Jute Germplasm by RAPD

  • Hossain, Mohammad Belayat;Haque, Samiul;Khan, Haseena
    • BMB Reports
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    • 제35권4호
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    • pp.414-419
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    • 2002
  • The genotype characteristic of cultivars was investigated, along with varieties of both of the jute species, Corchorus olitorius and Corchorus capsularis, in the germplasm collection at the Bangladesh Jute Research Institute (BJRI). DNA fingerprinting was generated for 9 different varieties and 12 accessions of jute cultivars by using random amplified polymorphic DNA(RAPD). A total of 29 arbitrary oligonucleotide primers were screened. Seven primers gave polymorphism within the varieties, and 6 primers detected polymorphism within the accessions that were tested. A dendrogram was engendered from these data, and this gave a distinct clustering of the cultivated species of jute. Therefore, we generated RAPD markers, which are species-specific. These primers can distinguish between C. olitorius and C. capsularis. From the dendrogram that we generated between the various members of these two species, we found the existing genetic classification that agrees with our molecular marking data. A different dendrogram showed that jute accessions could be clustered into three groups. These data will be invaluable in the conservation and utilization of the genetic pool in the germplasm collection.

Molecular Typing of Leuconostoc citreum Strains Isolated from Korean Fermented Foods Using a Random Amplified Polymorphic DNA Marker

  • Kaur, Jasmine;Lee, Sulhee;Sharma, Anshul;Park, Young-Seo
    • 산업식품공학
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    • 제21권2호
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    • pp.174-179
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    • 2017
  • For preliminary molecular typing, PCR-based fingerprinting using random amplified polymorphic DNA (RAPD) is the method of choice. In this study, 14 bacterial strains were isolated from different Korean food sources, identified using 16S rRNA gene sequencing, and characterized through RAPD-PCR. Two PCR primers (239 and KAY3) generated a total of 130 RAPD bands, 14 distinct PCR profiles, 10 polymorphic bands, one monomorphic band, and four unique bands. Dendrogram-based analysis with primer 239 showed that all 14 strains could be divided into seven clades out of which clade VII had the maximum of seven. In contrast, dendrogram analysis with the primer KAY3 divided the 14 L. citreum strains into four clades out of which clade IV consisted of a maximum of 10 strains out of 14. This research identified and characterized bacterial populations associated with different Korean foods. The proposed RAPD-PCR method, based on sequence amplification, could easily identify and discriminate the lactic acid bacteria species at the strain-specific level and could be used as a highly reliable genomic fingerprinting tool.

소형의 포자를 형성하는 Alternaria 균류의 분자생물학적 특징 (Molecular Characterization of Small-Spored Alternaria Species)

  • 김병련;박명수;조혜선;유승헌
    • 식물병연구
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    • 제11권1호
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    • pp.56-65
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    • 2005
  • 이 연구는 Alternaria속 균류 중에서 분생포자의 형태가 유사하여 분류, 동정이 매우 어려운 소형의 포자를 형성하는 11종의 Alternaria의 종간 유연관계와 분류체계를 확립하기 위하여 공시균들의 ribosomal DNA의 ITS 및 미토콘드리아 small submit 영역의 염기서열 분석, 그리고 URP primer에 의한 핵산지문분석을 실시하였다. 소형의 포자를 형성하는 11종 Alternaria속의 rDNA internal transcribed spacer(ITS) 영역과 미토콘드리아 small submit rDNA 의 염기서열을 분석하였던 바 A. infectoria를 제외한 10종의 Alternaria에서 100%의 상동성을 나타내었다. 이는 공시한 10종의 Alternaria가 유전적으로 매우 근연의 관계에 있음을 나타내며, 이 marker는 공시균들의 종구분에 이용할 수 없음을 나타내는 것이다. URP primer 10종을 공시하여 소형의 포자를 형성하는 Alternaria 균류의 핵산지문분석을 실시한 결과, 개개의 primer 로는 종간의 구분이 불가능하였으나 여러개의 primer를 종합하여 UPGMA분석을 실시할 경우 비록 종간 유사도는 높았디만 각각의 종은 독립된 cluster를 형성하여 종간 구별이 가능하였다. 자리공에서 분리한 Alternaria sp.는 URP-PCR 핵산지문 분석 결과 다른 Alternaria 종들과 차이가 인정됨으로 이 균은 미기록인 신종의 Alternaria로 사료되었다. A.infectoria는 다른 Alternaria 종들과 ITS 분석 및 URP-PCR 핵산지문분석에서 큰 차이를 보임으로서 뚜렷이 구별되는 종으로 판단되었다.

Application of rDNA-PCR Amplification and DGGE Fingerprinting for Detection of Microbial Diversity in a Malaysian Crude Oil

  • Liew, Pauline Woan Ying;Jong, Bor Chyan
    • Journal of Microbiology and Biotechnology
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    • 제18권5호
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    • pp.815-820
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    • 2008
  • Two culture-independent methods, namely ribosomal DNA libraries and denaturing gradient gel electrophoresis (DGGE), were adopted to examine the microbial community of a Malaysian light crude oil. In this study, both 16S and 18S rDNAs were PCR-amplified from bulk DNA of crude oil samples, cloned, and sequenced. Analyses of restriction fragment length polymorphism (RFLP) and phylogenetics clustered the 16S and 18S rDNA sequences into seven and six groups, respectively. The ribosomal DNA sequences obtained showed sequence similarity between 90 to 100% to those available in the GenBank database. The closest relatives documented for the 16S rDNAs include member species of Thermoincola and Rhodopseudomonas, whereas the closest fungal relatives include Acremonium, Ceriporiopsis, Xeromyces, Lecythophora, and Candida. Others were affiliated to uncultured bacteria and uncultured ascomycete. The 16S rDNA library demonstrated predomination by a single uncultured bacterial type by >80% relative abundance. The predomination was confirmed by DGGE analysis.

Universal Rice Primer(URP)에 의한 DNA 핵산지문법을 이용한 느타리의 유통 품종간 구분 (Differentiation Among Commercial Strains of Pleurotus spp. Based on DNA Fingerprinting Using Universal Rice Primer (URP))

  • 서경인;장갑열;유영복;박순영;김광호;공원식
    • 한국균학회지
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    • 제36권2호
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    • pp.130-137
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    • 2008
  • 본 연구에 사용된 느타리버섯류는 느타리속 8종 81개 품종으로 형태적 분류가 어려운 점 외에도 출처가 불확실한 품종이 재배되는 경우가 많아 정확한 품종구분이 요구되고 있다. 이러한 문제점을 해결하고자 국내에서 재배 유통되고 있는 느타리버섯류 81개 품종을 DNA 핵산지문법을 이용하여 유연관계를 분석한 결과 10 그룹으로 나누어졌으며, 이 중 느타리종에 속하는 70품종은 3 그룹으로 나누어졌다. 또한 이 그룹내에서 국내 주요품종인 원형, 수한, 춘추2호, 왕흑평과 동일하거나 유사한 것으로 나타난 품종이 많았다. I 그룹에 속하는 35개 품종 중 원형품종과 동일하거나 구별성이 인정되지 않는 품종은 4개 품종이었고, 왕흑평과는 6개의 품종이 동일한 것으로 나타났다. II 그룹의 23개 품종 중에는 21개의 품종이 수한과 구별성이 인정되지 않았다. 또한 II 그룹의 12개 품종 중 춘추2호와 유사 한 품종들은 총 6개였다.

Susceptibility Testing of Helicobacter pylori to Metronidazole and DNA Fingerprints of Resistant Strains in Singapore

  • HUA, JIESONG;KHAY-GUAN YEOH;PENGYUAN ZHENG;HAN CHONG NG;BOW HO
    • Journal of Microbiology and Biotechnology
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    • 제9권3호
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    • pp.328-333
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    • 1999
  • Susceptibility of 61 strains of Helicobacter pylori to metronidazole was examined by both the disk diffusion method using a cut-off of 15㎜ for resistance and the E test with a cut-off of 8㎎/l. The MIC/sub 50/ and MIC/sub 90/ by the E test were 2 ㎎/l and 256㎎/l, respectively. Metronidazole resistance was found in 22 (36%) out of the 61 H. pylori strains by the E test and in three additional strains by the disk diffusion method. Amongst the latter three isolates, the MICs by the E test were 4 ㎎/l, 6㎎/l, and 6㎎/l, respectively. These figures are one log₂ or half log₂ dilution lower than the cut-off of 8㎎/l recommended as resistance for the E test. All 22 metronidazole resistant H. pylori isolates by the E test that were subjected to random amplified polymorphic DNA (RAPD) fingerprinting showed different DNA fingerprints. Interestingly, >90% of resistant isolates possess two common DNA bands of 0.4 and 0.9 kb. This study demonstrates that the results of the disk diffusion method for testing H. pylori susceptibility to metronidazole correlates well with that of the E test. The criteria for interpretation need to be internationally standardized so that the results from different centers can be compared.

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Microsatellite 마커를 이용한 옥수수 품종 및 자식 계통에 대한 DNA Fingerprinting 분석 (DNA fingerprinting analysis of maize varieties and parental lines using microsatellite markers)

  • 권용삼
    • Journal of Plant Biotechnology
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    • 제43권3호
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    • pp.367-375
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    • 2016
  • 국내에서 육성된 옥수수 90 품종 및 자식 계통에 대하여 microsatellite 마커를 활용하여 DNA 프로파일 데이터베이스를 구축한 다음 공시품종에 따른 유전적 유사도 분석 및 품종식별력 검정에 대한 연구를 수행하였다. 옥수수 90품종을 100개의 microsatellite 마커로 검정하고 대립유전자의 패턴이 우수하고 다형성 정도가 높은 13개를 선정하여 분석하였을 때 대립유전자의 수는 5 ~ 24개까지 다양하게 분포하였고 평균 대립유전자의 수는 13.69개로 높았다. PIC 값의 경우도 0.716 ~ 0.942 범위에 속하였고 평균값은 0.865로 아주 높았다. 옥수수 90품종 및 계통에 대하여 UPGMA 분석에 의한 계통도를 작성하였을 때, 옥수수의 품종 유형 및 품종 육성 계보에 따라 5개의 대그룹으로 나누어졌다. 본 연구에서 구축됨 옥수수 자식계통 및 품종별 microsatellite DNA 프로파일 데이터베이스는 신품종과 기 육성된 품종과 유전적 유사도 분석이 가능하기 때문에 품종보호출원시 대조품종 선정 및 품종진위성과 관련된 종자분쟁에 매우 유용하게 활용될 수 있을 것이다.

Molecular Typing of Pseudomonas aeruginosa by Randomly Amplified Polymorphic DNA

  • Byoung-Seon Yang
    • 대한의생명과학회지
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    • 제9권4호
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    • pp.183-187
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    • 2003
  • Pseudomonas aerugionsa is a commonly isolated nosocomial pathogen. DNA fingerprinting of P. aerugionsa is examined by randomly amplified polymorphic DNA (RAPD). In this study, P. aeruginosa were isolated from environmental and clinical specimens and the molecular typing of the microorganisms was investigated by RAPD. Thirty strains of P. aeruginosa were selected from the strains isolated formerly and submitted for type identification to the University Hospital. 15 strains of P. aeruginosa were received from Chungnam University Hospital and 14 strains from Gyeongsang University Hospital. DNA of P. aeruginosa was extracted by Qiagen genomic DNA kit. PCR mixtures were set up and incubated, Reactions mixtures were made to be optimal for P. aeruginosa. RAPD typing analysis was carried out by the multivariate statistical program (MVSP) V3.0. RAPD type I was the most common pattern and included 23 strains. Most of strains from Gyeongsang University Hospital belonged to RAPD type lb and 15 strains from Chungnam University Hospital to RAPD type I or II. RAPD typing of P. aeruginosa isolated from the environmental and clinical specimens was very simple and reproducible.

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