• 한국육종학회지
• /
• 제43권4호
• /
• pp.265-272
• /
• 2011

This study is to generate SCARs markers for identification of Perilla species. A SCAR is a genomic DNA fragment at a single genetically defined locus that is identified by PCR amplification using a pair of specific oligonucleotide primers. We derived SCARs by sequencing and cloning the both ends of the amplified products of RAPD markers. Sixteen sequence-specific primers were synthesized from eight RAPD markers, which were completely sequenced. We developed the species-specific SCAR markers which could be used successfully in detecting genetic variation in four Perilla species. These markers could be used to verify species-origins of various forms of Perilla germplasms.

• 한국동물위생학회지
• /
• 제41권3호
• /
• pp.149-155
• /
• 2018

Salmonella Enteritidis (S. Enteritidis) are found in animals, humans, and environment. In addition, S. Enteritidis draws attention to the public health concerns due to carriage of antibiotic resistance traits. For these reasons, the prevalence and antibiotic resistance patterns of S. Enteritidis are significant issues with regard to public health. To address this issues, a total of 24 strains of S. Enteritidis from 164 samples collected from several slaughterhouses in Gyeong-Nam province in order for antibiotic resistance profiles. Subsequently, we characterized the genotyping by random amplification polymorphic DNA (RAPD)-PCR. As a result, very high level of resistance to protein synthesis inhibition antibiotics and most isolates were susceptible to others. Six random primers were used for RAPD-PCR to reveal genotypes of S. Enteritidis isolates. One of the primer, P1245, generated 147 distinct RAPD-PCR fragments ranging from 400~3000 bp. The number of RAPD-PCR products ranged from 4 to 8 for this primer. The RAPD-PCR fragments could be placed these strains into 3 subgroups and 2 classes by UPGMA cluster analysis. Interestingly, several S. Enteritidis that isolated from different slaughterhouses showed same genotype. These results showed only limited genetic variation among the isolates, those were grouped into a few different patterns of antibiotic resistance.

• 한국약용작물학회지
• /
• 제19권3호
• /
• pp.162-169
• /
• 2011

The rhizomes and herbal medicines originating from Acorus gramineus, A. calamus, A. tatarinowii, and A. gramineus var. pusilus, show significant similarity, and the correct identification of species is very difficult. Random Amplified Polymorphic DNA (RAPD) and Sequence Characterized Amplified Region (SCAR) were used to develop a reliable method for identification of these four species. Several distinct SCAR markers were developed from species-specific RAPD amplicons for each species. Furthermore, a useful molecular marker was established for multiplex-PCR, in order to the four species could be distinguished concurrently. These markers allow efficient and rapid identification of closely-related Acorus species and will be useful for standardization of herbal medicines.

• Mycobiology
• /
• 제38권1호
• /
• pp.17-25
• /
• 2010

The common split-gilled mushroom, Schizophyllum commune is found throughout the world on woody plants. This study was initiated to evaluate conditions for favorable vegetative growth and to determine molecular phylogenetic relationship in twelve different strains of S. commune. A suitable temperature for mycelial growth was obtained at $30^{\circ}C$. This mushroom grew well in acidic conditions and pH 5 was the most favorable. Hamada, glucose peptone, Hennerberg, potato dextrose agar and yeast malt extract were favorable media for growing mycelia, while Lilly and glucose tryptone were unfavorable. Dextrin was the best and lactose was the less effective carbon source. The most suitable nitrogen sources were calcium nitrate, glycine, and potassium nitrate, whereas ammonium phosphate and histidine were the least effective for the mycelial growth of S. commune. The genetic diversity of each strain was investigated in order to identify them. The internal transcribed spacer (ITS) regions of rDNA were amplified using PCR. The size of the ITS1 and ITS2 regions of rDNA from the different strains varied from 129 to 143 bp and 241 to 243 bp, respectively. The sequence of ITS1 was more variable than that of ITS2, while the 5.8S sequences were identical. A phylogenetic tree of the ITS region sequences indicated that the selected strains were classified into three clusters. The reciprocal homologies of the ITS region sequences ranged from 99 to 100%. The strains were also analyzed by random amplification of polymorphic DNA (RAPD) with 20 arbitrary primers. Twelve primers efficiently amplified the genomic DNA. The number of amplified bands varied depending on the primers used or the strains tested. The average number of polymorphic bands observed per primer was 4.5. The size of polymorphic fragments was obtained in the range of 0.2 to 2.3 kb. These results indicate that the RAPD technique is well suited for detecting the genetic diversity in the S. commune strains tested.

• 한국자원식물학회지
• /
• 제27권3호
• /
• pp.236-241
• /
• 2014

A sex-linked random amplified polymorphic DNA (RAPD) marker was identified from Asparagus officinalis L. and was converted into a sequence-characterized amplified regions (SCAR) marker for the large-scale screening of male and female plants. A total of 100 arbitrary decamer oligonucleotide primers were used for the RAPD analysis. Among them, the primer UBC347 amplified one female-specific 400 base pair DNA. Subsequently, the amplified RAPD fragment was cloned and sequenced. The fragment was abundant in AT and shared sequence homology with retrotransposon elements. On the basis of the sequence obtained, a pair of SCAR primer was designed. The amplification product, named F400, was the same size as the respective RAPD fragment from which it was derived. The F400 SCAR marker resulted to be female-specific in the three asparagus varieties tested in this study. This SCAR marker can be used for an early and rapid identification of female and male plants during breeding programs of asparagus.

• Mycobiology
• /
• 제30권3호
• /
• pp.139-145
• /
• 2002

Gibberella fujikuroi is species complex. This species complex includes Fusarium tabacinum, F. moniliforme(=F. verticillioides), F. nygamai, F. proliferatum as well as F. subglutinans. Our objective was to develop a technique to differentiate between isolates of F. subglutinans, F. proliferatum and F. verticillioides. Thirty-two strains of F. subglutinans, six strains from F. verticillioides and five strains of F. Proliferatum isolated from maize in Austria were studied using random amplified polymorphic DNA(RAPD). F. subglutinans strains clustered very closely, with similarity ranging from $87{\sim}100%$. On the other hand, all the amplification patterns of F. verticillioides were identical, as well as in the case of F. proliferatum. Our results indicated that these Fusaria species are distinct species and hence RAPD markers can be quick and reliable for differentiating them.

• Food Science and Biotechnology
• /
• 제17권6호
• /
• pp.1171-1177
• /
• 2008

This study was undertaken to classify Enterobacter sakazakii isolates from 13 powdered infant formula products, 25 powdered weaning diet products, and 33 weaning diet ingredients on polymerse chain reaction (PCR) methods. The numbers of the isolates from 1 powdered infant formula product, 7 powdered weaning diet products, and 6 weaning diet ingredients were 1, 14, and 8, respectively. The contaminated ingredients were 1 rice powder, 2 millet powders, 2 vegetable powders, and 1 fruit and vegetable premix. PCR with the primer of repetitive extragenic palindromic element (REP-PCR) and random amplification of polymorphic DNA(RAPD) were effective in discriminating among the isolates, but tRNA-PCR and PCR with the primer of l6S-23S internal transcribed spacer (ITS-PCR) were not. Some of E. sakazakii isolates from vegetable powders, fruit and vegetable premix, and millets powders were classified into the clonal groups based on the DNA patterns in the REP-PCR and RAPD analysis. A close genetic relationship among the isolates from some of the powdered weaning diet products and the rice powder was also detected in the cluster analysis based on the DNA patterns in RAPD.

• The Plant Pathology Journal
• /
• 제22권1호
• /
• pp.36-45
• /
• 2006

Twenty isolates of Didymella bryoniae were isolated from infected cucurbit plants in various growing areas of southern Korea in 2001 and 2002. Random Amplified Polymorphic DNA (RAPD) group [RG] I of D. bryoniae was more virulent than RG IV to watermelon. Virulence of the RG I isolate was strong to moderate to cucumber, whereas that of the RG IV varied from strong, moderate to weak. Two hundred seventy-three amplified fragments were produced with 40 primers, and were analyzed by a cluster analysis using UPGMA method with an arithmetic average program of NTSYSPC. At the distance level of 0.7, two major genomic DNA RAPD groups were differentiated among 20 isolates. The RG I included 7 isolates from watermelon and one isolate from melon, whereas the RG IV included 12 isolates from squash, cucumber, watermelon and melon. Amplification of internal transcribed spacer (ITS) region and small subunit rRNA region from the 20 isolates yielded respectively a single fragment. Restriction pattern with 12 restriction enzymes was identical for all isolates tested, suggesting that variation in the ITS and small subunit within the D. bryoniae were low. Amplification of the genomic DNAs of the tested isolates with the sequence characterized amplified regions (SCAR) primer RG IF-RG IR specific for RG I group resulted in a single band of 650bp fragment for 8 isolates out of the 20 isolates. Therefore, these 8 isolates could be assigned into RG I. The same experiments done with RG IIF-RG IIR resulted in no amplified PCR product for the 20 isolates tested. An about 1.4 kb-fragment amplified from the RG IV isolates was specifically hybridized with PCR fragments amplified from genomic DNAs of the RG IV isolates only, suggesting that this PCR product could be used for discriminating the RG IV isolates from the RG I isolates as well other fungal species.

• Mycobiology
• /
• 제35권3호
• /
• pp.154-156
• /
• 2007

A database application, namely MushBase, has been built based on Microsoft Access in order to store and manage different kinds of data about mushroom biological information of species, strains and their physiological characteristics such as geometries and growth condition(s). In addition, it is also designed to store another group of information that is experimental data about mushroom classification by Random Amplification of Polymorphic DNA (RAPD). These two groups of information are stored and managed in the way so that it is convenient to retrieve each group of data and to cross-refer between them as well.

• 한국자원식물학회지
• /
• 제13권1호
• /
• pp.1-10
• /
• 2000

재배되고 있는 22 페칸종간의 RAPD분석을 한 결과, Agarose gel상에서 primer당 평균 6개의 DNA단편이 증폭되었다. 증폭된 DNA 단편의 크기 는 100bp에서 1500bp의 범위에 위치하였다. 페칸종간의 유연 관계를 분석하기에 적합한 primer를 선발한 결과 OPA-02, OPA-10, OPA-12, OPB-01이 최적이었다. 4종의 primer를 이용하여 증폭한 PCR산물을 1.5% Agarose gel상에 분획하여 단편의 종류를 분석한 결과 22의 페칸종은 5개의 그룹으로 구분 할 수 있었다. 40종 primer로부터 증폭된 466 DNA단편을 기초로하여 유전적 근연계수를 계산하였던 결과 유사도 값이 가장큰 것은 C. flacra와 Black walnut로 0.90를 나타났으며, Kiowa와 Red hickory, C. tomentosa, C. flacra, Black walnut간에는 유사도 값이 0.31로 가장 작았다. 선발된 4종의 primer를 이용하여 증폭시킨 PCR산물을 Polyacrylamide gel상에 분획한 후 검출된 DNA단편을 분석하였다. 유사도 값이 가장 큰 것은 그룹 V의 Red hickory, C. tomentosa, C. flacra, Black walnut간으로 1.0이었고, Farley와 Pawnee간과 Sturya와 Clarke간은 공히 0.98를 나타내었다. Polyacrylamide gel분획 후 은염색하여 단편을 검출하는 것은 Agarose gel에 비하여 시간, 기술, 경비가 요구되지만 보다 정확한 유전적 배경을 설명할 수 있다고 생각되었다. 또한 Agarose gel 분석, Polyacrylamide gel 분석 및 주성분 분석법에서 Farley, C. tomentosa, C. flacra, Black walnut, C. corpiformis만이 동일 그룹에서 이탈되지 않았다.