• Journal of Life Science
• /
• v.32 no.8
• /
• pp.595-600
• /
• 2022

Water dropworts, Oenanthe javanica and O. javanica var. japonica are called "minari" in Korea and are eaten as a vegetable. Cicuta virosa is common European water hemlock and has toxic properties, such as cicutoxin. Molecular variations of water dropwort species in Korea were investigated using random amplified polymorphic DNA (RAPD). The six populations were studied with 10 primers (Operon, OPB) for RAPD analysis. The 72 DNA fragments (bands) were found among six populations. Among these 72 bands, 61 (84.7%) bands were polymorphic. The typical populations of Cicuta virosa in Korea were small, isolated, and patchily distributed for natural populations and they maintained a high level of genetic diversity. However, when cultivated populations of O. javanica var. japonica were large and widely grown in rice paddies as vegetables, they maintained a lower genetic diversity than those of C. virosa and wild populations of O. javanica. Although the diversity indices of wild populations were shown to be higher than those of cultivated populations, no significant difference for measures of genetic variability was shown. Total genetic diversity value (H_T) was 0.342. The interlocus variation in the within-population genetic diversity (H_S) was 0.201. The proportion of total genetic variation due to differences among populations (G_ST) range was 0.414, indicating that 41.4% of the total variation was among populations. In conclusion, the RAPD technique was a useful method for discrimination between C. virosa and O. javanica. In addition, RAPD-OPB markers could further distinguish the strains from different food sources.

• The Korea Journal of Herbology
• /
• v.24 no.4
• /
• pp.115-120
• /
• 2009

Objectives : Due to the morphological similarity and frequent occurrence of intermediate forms as well as morphological variations of aerial part, the correct identification between Rhei Radix et Rhizoma and Rhei Undulatai Rhizoma is very difficult. To develop a reliable method for correct identification and improving the quality standards of Rhei Radix et Rhizoma and Rhei Undulatai Rhizoma, we analyzed RAPD and developed SCAR marker. Methods : To amplify target DNA at the genomic level, 32 Operon 10-mer random primers were applied with four Rheum species, R. officinale, R. palmatum, R. tanguticum and R. undulatum. The nucleotide sequences were determined and species-specific primers were prepared depending on the species-specific RAPD amplicons after subcloned into the pGEM-Teasy vector. To develop the SCAR markers, species-specific PCR amplification and multiplex-PCR were carried out using the single species-specific primer pairs and combinations of them, respectively. Results : We used RAPD analysis of four Rheum plant species to obtain several species-specific RAPD amplicons. From nucleotide sequences of these RAPD amplicons, we developed two SCAR markers that amplified 314 bp and 390 bp DNA fragments in only R. undulatum but not in R. officinale, R. palmatum, R. tanguticum and R. undulatum, for distinguishing Rhei Undulatai Rhizoma and Rhei Radix et Rhizoma. Furthermore, we established SCAR markers for the simultaneous discrimination of the three species within a single reaction by using multiplex-PCR. Conclusions : These genetic markers can be used for the efficient discrimination of plants species and commercial herbal medicines between Rhei Undulatai Rhizoma and Rhei Radix et Rhizoma, to ultimately prevent indiscriminate distribution and prescription of these herbal medicines.

• Korean Journal of Weed Science
• /
• v.18 no.1
• /
• pp.76-83
• /
• 1998

Echinochloa species maintained by selling for more than 10 years were classified using random amplified polymorphic DNAs(RAPDs) analysis. Seventy-four decamer of randomly sequence markers were used to classify intraspecific variation irt Echinochloa species. The number of amplification products increased with increasing GC content of the primer in the range between 60% and 70% GC. Single-base substitutions of a primer altered amplification, providing new polymorphisms. The size of amplified DNA was mostly between 0.40kbp and 1.4kbp with the most common bands at 1.1kbp. Echinochloa species were detected with 6 primers which generated 26 polymorphic amplified DNAs. By hierarchical cluster analysis, Echinochloa species collected in Korea were divided into three groups. These results revealed that RAPD markers are useful tools for the determination of genetic variations in Echinochloa species.

• Journal of Microbiology and Biotechnology
• /
• v.22 no.6
• /
• pp.742-753
• /
• 2012

Copper-containing compounds are introduced into the environment through agricultural chemicals, mining, and metal industries and cause severe detrimental effects on ecosystems. Certain microorganisms exposed to these stressors exhibit molecular mechanisms to maintain intracellular copper homeostasis and avoid toxicity. We have previously reported that the soil bacterial isolate Achromobacter sp. AO22 is multi-heavy metal tolerant and exhibits a mer operon associated with a Tn21 type transposon. The present study reports that AO22 also hosts a unique cop locus encoding copper homeostasis determinants. The putative cop genes were amplified from the strain AO22 using degenerate primers based on reported cop and pco sequences, and a constructed 10,552 base pair contig (GenBank Accession No. GU929214). BLAST analyses of the sequence revealed a unique cop locus of 10 complete open reading frames, designated copSRABGOFCDK, with unusual separation of copCD from copAB. The promoter areas exhibit two putative cop boxes, and copRS appear to be transcribed divergently from other genes. The putative protein CopA may be a copper oxidase involved in export to the periplasm, CopB is likely extracytoplasmic, CopC may be periplasmic, CopD is cytoplasmic/inner membrane, CopF is a P-type ATPase, and CopG, CopO, and CopK are likely copper chaperones. CopA, B, C, and D exhibit several potential copper ligands and CopS and CopR exhibit features of two-component regulatory systems. Sequences flanking indicate the AO22 cop locus may be present within a genomic island. Achromobacter sp. strain AO22 is thus an ideal candidate for understanding copper homeostasis mechanisms and exploiting them for copper biosensor or biosorption systems.

• Journal of Microbiology and Biotechnology
• /
• v.17 no.2
• /
• pp.287-296
• /
• 2007

A Lactobacillus paraplantarum strain producing a bacteriocin was isolated from kimchi using the spot-on-the lawn method and named L. paraplantarum C7 [15]. The bacteriocin, paraplantaricin C7, was found to inhibit certain Lactobacillus strains, including L. plantarum, L. pentosus, and L. delbrueckii subsp. lactis. It also inhibited Enterococcus faecalis, yet did not inhibit most of the other LAB (lactic acid bacteria) tested. The maximum level of paraplantaricin C7 activity was observed under the culture conditions of $25^{\circ}C$ and a constant pH of 4.5. Paraplantaricin C7 retained 90% of its activity after 10 min of treatment at $100^{\circ}C$ and remained stable within a pH range of 2-8. Based on a culture supernatant, paraplantaricin C7 was purified by DEAE-Sephacel column chromatography and $C_{18}$ reverse-phase HPLC. SDS-PAGE and activity staining were then conducted using the purified paraplantaricin C7, and its molecular mass determined to be about 3,800 Da. The 28 N-terminal amino acids from the purified paraplantaricin C7 were determined, and the structural gene encoding paraplantaricin C7, ppnC7, was cloned by PCR using degenerate primers based on the N-terminal amino acid sequence. The nucleotide sequences for ppnC7 and other neighboring orfs exhibited a limited homology to the previously reported plantaricin operon genes. Paraplantaricin C7 is a novel type II bacteriocin containing a double glycine leader sequence.

• Plant Resources
• /
• v.2 no.1
• /
• pp.22-25
• /
• 1999

Molecular markers are useful to confirm the hybridity of F1 plant derived from cross of two homozygous parents with similar morphological traits. RAPD markers were used to test F1 hybrid plant obtained from cross of two homozygous soybean (Glycine max) parents. Fl plant for cross I was made from the mating of Hobbit87 (female) and L63-1889 (male) and Fl plant for cross II was obtained from the mating of H1053 (female) and L63-1889 (male). Selfing plant per each cross was also obtained. Among 20 Operon primers used, OPA04 and OPA09 show polymorphism between cross I and II parent. Band in size 1Kb of OPA04 and 2.1Kb of OPA09 primer was polymorphic band. This fragment identified Fl hybrid plant and selfing plant in cross I and II. Female parent Hobbit87 in cross I and H1053 in cross II has no this fragment (recessive allele). However, male parent L63-1889 and Fl hybrid plant in cross I and II has this size of polymorphic band (dominant allele). This indicated that Fl hybrid and selfing plants were detected by RAPD marker before phenotypic marker would be used to identify Fl hybridity. Amplification products of selfing plant for cross I and II were completely same to the those of female parent. When mature, flower color of Fl hybrid plant in cross I and II was purple and flower color of selfing plant in cross I and II was white. Purple flower is dominant trait. Fl hybridity was successfully detected at very early growth stage using RAPD marker. Therefore, RAPD marker can be used broadly to confirm Fl hybridity in many crops.

• Journal of Mushroom
• /
• v.13 no.1
• /
• pp.79-83
• /
• 2015

In this study, SCAR marker that differentiates Pleurotus eryngii strains with higher ${\beta}$-glucan from control strain was developed. Genomic DNAs of 9 control strains of Pleurotus eryngii and 9 Pleurotus eryngii strains with higher ${\beta}$-glucan were analyzed by bulked segregant analysis (BSA) using randomly amplified polymorphic DNA (RAPD). One-hundred twenty RAPD primers were screened on bulked DNA samples and a unique DNA fragment with the size of 91 bp was yielded by OP-R03 primer from the Pleurotus eryngii strains with higher ${\beta}$-glucan. A sequence characterized amplified region (SCAR) marker, designated as OP-R03-1-F and OP-R03-1-R, was designed on the basis of the determined sequence. The PCR analysis with the OP-R03-1 primer showed that this SCAR marker can clearly distinguish the Pleurotus eryngii strains with higher ${\beta}$-glucan from the control strains.

• Journal of Mushroom
• /
• v.12 no.3
• /
• pp.226-231
• /
• 2014

In this study, SCAR marker that differentiates Pleurotus eryngii strains adaptable to high-temperature from control strain was developed. Genomic DNAs of 7 control strains of Pleurotus eryngii and 7 Pleurotus eryngii strains adaptable to high-temperature were analyzed by bulked segregant analysis (BSA) using randomly amplified polymorphic DNA (RAPD). Onehundred twenty RAPD primers were screened on bulked DNA samples and a unique DNA fragment with the size of 385 bp was yielded by OP-A06 primer from the Pleurotus eryngii strains adaptable to high-temperature. A sequence characterized amplified region (SCAR) marker, designated as OP-A06-1-F and OP-A06-1-R, was designed on the basis of the determined sequence. The PCR analysis with the OP-A06-1 primer showed that this SCAR marker can clearly distinguish the Pleurotus eryngii strains adaptable to high-temperature from the control strains.

• Korean Journal of Agricultural Science
• /
• v.28 no.1
• /
• pp.1-7
• /
• 2001

In this study we evaluated genetic divergence among six Tongil-type rice varieties and assessed the relationship between genetic distance and hybrid performance in all possible non-reciprocal crosses between them. The 15 F1 hybrids along with the six parents were evaluated for eight traits of agronomic importance including yield in a replicated field trial. The six parents were examined for DNA polymorphism using 120 random decamer oligonucleotide primers. A total of 168 polymorphic variants were generated and based on the polymorphism data, genetic distances (GDs) ranged from 0.157 to 0.383. Heterosis was observed in hybrids for most of the traits, and yield exhibited the highest heterosis among the eight traits examined. The correlation values of GDs with F1 performance were not significant. Also the correlations of GDs with midparent and better-parent heterosis were not significant except for spikelets per panicle. Our results have indicated that GDs based on the RAPDs markers may not be useful for predicting heterotic combinations in Tongil-type rice and are supportive of the idea that the level of correlations between hybrid performance and genetic divergence is dependent on the germlplasm employed.

• Journal of Mushroom
• /
• v.11 no.3
• /
• pp.171-176
• /
• 2013

Genomic DNAs of psychrophilic strains of Pleurotus eryngii were analyzed by randomly amplified polymorphic DNA (RAPD) using OP-A, OP-B, OP-L, OP-P, OP-R and OP-S3 primers to develop the strain-specific DNA marker. A unique DNA fragment with the size of 480 bp was yielded by OP-S3 primer from the psychrophilic strain. A sequence characterized amplified region (SCAR) marker, designated as OP-S3-1, was designed on the basis of the determined sequence. The PCR analysis with the OP-S3-1 primer showed that this SCAR marker can clearly distinguish the psychrophilic strains from the control strains.