• Journal of Forest and Environmental Science
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• v.25 no.1
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• pp.57-65
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• 2009

Ficus deltoidea Jack is an important and popular medicinal plant species found in the Malaysia. Plants are being collected and used based on morphology and authentication to prevent adulteration is not in practice. In this study, twenty-six accessions of F. deltoidea Jack were collected from Kelantan and Terengganu states of Peninsular Malaysia to examine their genetic similarities and differences using randomly amplified polymorphic DNA (RAPD) technique. Out of 20 arbitrary primers, two primers (D-10 and D-11) were selected which produced reliable DNA polymorphism. D-10 and D-11 primers generated 138 RAPD bands ranging from 250 bp to 3000 bp. Ninety-nine of them were polymorphic loci (72%) and thirty-nine were nonpolymorphic loci (28%). A total of 56 bands with polymorphic loci were amplified with primer D-10 and analyzed by cluster analysis and UPGMA to present a dendrogram depicting the degree of genetic relationship among 26 accessions. Eight RAPD markers were sequenced to determine their identity. RAPD analysis showed the genetic diversity among 26 accessions of F. deltoidea Jack. The RAPD profile and RAPD marker sequences reported in this paper could be used in plant and/or plant material authentication. This study also suggested that RAPD can be a useful technique to study DNA polymorphism in F. deltoidea Jack.

• 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.

• Korean Journal of Ichthyology
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• v.18 no.1
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• pp.1-11
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• 2006

Genomic DNA isolated from two geographical populations of pond-smelt (Hypomesus nipponensis) was amplified for RAPD (randomly amplified polymorphic DNA) analysis. The populations were obtained from Chungju (CJ), in the inland area, and Dangjin (DJ), in the vicinity of the West Sea in Korea. Seven arbitrarily selected primers, OPB-06, OPB-10, OPB-13, OPB-17, OPC-09, OPC-17 and OPC-20, were used to generate the shared loci, polymorphic, and specific loci. Three hundred and eighty-three loci observed per primer were identified in the CJ population, and 287 were identified in the DJ population. Among them, 91 polymorphic loci or 23.8% were polymorphic in the CJ population, and 47 (16.4%) in the DJ population. The number of shared loci observed was 198 in the CJ population and 176 in the DJ population. Forty-four and 75 specific loci were detected in the CJ and DJ populations, respectively. Especially, 99 numbers of shared loci by the two populations, with an average of 14.1 per primer, were observed in the two pond-smelt populations. The average bandsharing value between the two geographical pond-smelt populations was $0.700{\pm}0.008$, ranging from 0.600 to 0.846. Compared separately, the bandsharing value of individuals within the CJ population was higher than that of the DJ population. The dendrogram obtained using the data from the seven primers indicated three genetic clusters: cluster 1, CJ 01, 02, 03, 04, 05, 06, 07, 08, 09, 10, and 11; cluster 2, DJ 01, 02, 03, 04, 05, 06, 07, 08, and 09; and cluster 3, DJ 10 and 11. The genetic distance between the two geographical populations ranged from 0.040 to 0.545. Thus, RAPD-PCR analysis revealed a significant genetic distance between the two pond-smelt populations.

• Proceedings of the Korean Society for Food Science of Animal Resources Conference
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• 2000.11a
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• pp.59-75
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• 2000

This study was carried out to develop a DNA marker for identifying between Korean cattle (Hanwoo) and other breeds. First experiment was performed to isolate Hanwoo specific DNA marker at sequence characterized amplified regions (SCARs). Five breeds of cattle including Hanwoo, Holstein, Hereford, Angus and Charolais were represented with the from 8 to 20 individuals. Fourteen primers of 300 arbitrary primers of 10 nucleotides showed reproducible polymorphism across the breeds. An amplified band of 0.9 kb in the primer MG-3 showed the specificity to Holstein breed. And MG-6 and MG-12 detected the Hereford and Hanwoo specific markers at the size of 2.0 kb and 1.0 kb, respectively. A 1.0 kb band of MG-12 was cloned and sequenced. A SCAR primer was designed based on the obtained sequences. It was possible to identify the Hanwoo from Holstein breed. Second experiment was carried out to observe the genotype frequencies of MC1R in 1,044 samples of imported beef and eight different cattle breeds including Hanwoo, Holstein, Angus, Brown-Swiss, Charolais, Limousin, Simmental and Hereford. The primers for the amplification of bovine MC1R gene were designed based on a bovine MC1R gene sequence (GenBank accession no.Y19103). A size of 350 bp was amplified by polymerase chain reaction(PCR), digested with two different restriction enzyme, BsrFI and MspA II, and electrophoresed in 2.5% Metaphore agarose gel for determination of genotypes. Genotype frequencies of Hanwoo were 0.10 in E+e and 0.90 in ee. Allele ED was shown in all of Holstein and Angus breeds tested which have black coat color phenotypes. We suggested that SCAR marker and the bovine MC1R gene could be used as a DNA marker for distinguishing beef between Hanwoo and Holstein.

• Journal of Life Science
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• v.9 no.6
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• pp.671-676
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• 1999

RAPD analysis using random primers were tried to evaluate the genetic variation and diversity of the nine garlic cultivars including two foreign varieties. Thirty-two primers out of 70 primers screened were used to amplify genomic DNA of garlic cultivars using polymerase chain reaction(PCR). Among a total of 151 bands amplified by 32 primers, 125 polymorphic bands were subjected to analysis for genetic relationship of garlic cultivars. The estimated size of amplified PCR products were in the range of 932 to 4,060 base pairs. Nine garlic cultivars were classified into two groups, such as group I corresponded to Changnyung and Hungary cultivars, and group II, Namdo, Sandong from China, Yecheon, Euiseong, Youngweol, Danyang, Jeongsun cultivars, with the genetic distance value of 0.271. The major ecological types of garlics, so called southern and northern types, was grouped in the genetic distance value of 0.200. The results presented in this study suggest that RAPD analysis are likely to be useful for identification of cultivars and evaluation of genetic origin in garlics.

• The Korean Journal of Mycology
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• v.20 no.4
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• pp.315-323
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• 1992

The effects of several parameters on PCR amplification in using RAPD were studied. The results of this study suggest that approximately 15 ng of genomic DNA in $20\;{\mu}l$ of reaction mixture results in discrete and reproducible PCR products. In addition, the results indicate that concentration or amounts of reaction components studied are highly inter-dependent in their effects, and RNA can interfere severely with PCR amplification. Suitable concentrations or amounts of reaction components were found to be 30 ng of 10-mer primer, $200\;{\mu}M$ of dNTP, 0.001% gelatin 1.5 mM $MgCl_2$, 10 mM Tris-Cl (pH 8.8), 50 mM KCl, 0.1% Triton X-100, 2 units of Taq DNA polymerase, and 15 ng of RNase-treated genomic DNA in $25\;{\mu}l$ of reaction mixture.

• BMB Reports
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• v.37 no.2
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• pp.213-222
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• 2004

A randomly amplified polymorphic DNA (RAPD) analysis was used to identify the species- and population-specific markers of abalone; Haliotis asinina, H. ovina, and H. varia in Thai waters. Fifteen species-specific and six population-specific RAPD markers were identified. In addition, an 1650 bp band (UBC195) that was restricted to H. ovina from the Gulf of Thailand (east) was also found. All of the specific RAPD markers were cloned and sequenced. Twenty pairs of primers were designed and specificity-tested (N = 12 and 4 for target and non-target species, respectively). Seven primer pairs (CUHA1, 2, 4, 11, 12, 13, and 14) were specifically amplified by H. asinina DNA, whereas a single pair of primers showed specificity with H. ovina (CUHO3) and H. varia (CUHV1), respectively. Four primer pairs, including CUHA2, CUHA12, CUHO3, and CUHV1, were further examined against 216 individuals of abalone (N = 111, 73, and 32, respectively). Results indicated the species-specific nature of all of them, except CUHO3, with the sensitivity of detection of 100 pg and 20 pg of the target DNA template for CUHA2 and CUHA12 and CUHV1, respectively. The species-origin of the frozen, ethanol-preserved, dried, and boiled H. asinina specimens could also be successfully identified by CUHA2.

• Food Science and Biotechnology
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• v.17 no.6
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• pp.1171-1177
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• 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.

• Proceedings of the Korean Society of Fisheries Technology Conference
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• 2001.05a
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• pp.334-335
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• 2001

Common carp (Cyprinus carpio) and Israeli carp(C. carpio) samples were obtained from a aquaculture facility in the Kunsan National University, Korea. Genomic DNA was isolated from the common carp and Israeli carp representing genetic characteristics and genomic polymorphisms by polymerase chain reaction amplification of DNA as arbitrary primers. There were observed a total of 90 species-specific genetic markers within Israeli carp. On average, each random RAPD primer produced amplified 7.9 products from 1 to 17 bands. An average genetic similarity within Israeli carp showed -.60$\pm$0.05. The average level of bandsharing was some 0.57$\pm$0.03 between common carp and Israeli carp. Accordingly, two carp species were genetically a little distant. The electrophoretic analysis of PCR-RAPD proudcts showed high levels of variation between two fish species. The RAPD polymorphism generated by primer may be used as a genetic marker for species or lines identification in important aquacultural carp.

• Journal of Korean Society of Forest Science
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• v.87 no.3
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• pp.422-428
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• 1998

Polymerase chain reaction(PCR)-based inter-simple sequence repeats(I-SSR) markers were analyzed in 48 megagametophytes of a single tree of Abies koreana $W_{ILS}$. Nineteen of the 35 primers, screened with 6 megagametophyte DNA and produced the clearest amplification products in the preliminary experiment, were used for PCR with 48 megagametophyte DNAs sampled from a single tree. On the basis of the chi-square test, a total of 51 amplicons, amplified by the 19 primers, were revealed to be segregated according to the Mendelian ratio(i.e., 1 : 1 segregation ratio) in the 48 megagametophytes at 5% significance level. Based on the linkage analysis, the observed 51 Mendelian loci turned out to be unlinked each other, which suggested that they are evenly distributed in the genome. However, majority of RAPD markers are known to belong to the independent linkage blocks, which frequently results in the amplification of RAPD markers from the restricted regions of the genome. Owing to the nature of even distribution of the 51 loci observed in this study, the I-SSR markers could give better resolution of estimating genetic diversity from the whole genome than RAPD markers. And I-SSR markers are also more suitable than RAPD markers for reconstructing phylogenetic relationship by a cladistic method which requires to fulfil the assumption of independent evolution of the different characters.