• Journal of Plant Biotechnology
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• v.47 no.2
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• pp.131-140
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• 2020

Solanum stoloniferum, one of the wild tetraploid Solanum species belonging to the Solanaceae family, is an excellent resource for potato breeding owing to its resistance to several important pathogens. However, the sexual hybridization of S. stoloniferum with S. tuberosum (potato) is hampered due to the sexual incompatibility between the two species. To overcome this and introgress the various novel traits of S. stoloniferum in cultivated potatoes, cell fusion can be performed. The identification of the fusion products is crucial and can be achieved with the aid of molecular markers. In this study, the chloroplast genome sequence of S. stoloniferum was obtained by next-generation sequencing technology, and compared with that of six other Solanum species to identify S. stoloniferum-specific molecular markers. The length of the complete chloroplast genome of S. stoloniferum was found to be 155,567 bp. The structural organization of the chloroplast genome of S. stoloniferum was similar to that of the six other Solanum species studied. Phylogenetic analysis of S. stoloniferum with nine other Solanaceae family members revealed that S. stoloniferum was most closely related to S. berthaultii. Additional comparison of the complete chloroplast genome sequence of S. stoloniferum with that of five Solanum species revealed the presence of six InDels and 39 SNPs specific to S. stoloniferum. Based on these InDels and SNPs, four PCR-based markers were developed to differentiate S. stoloniferum from other Solanum species. These markers will facilitate the selection of fusion products and accelerate potato breeding using S. stoloniferum.

• Journal of The Korean Society of Grassland and Forage Science
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• v.18 no.4
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• pp.277-284
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• 1998

Random amplified polymorphic DNA (RAPD) analysis was used to detect the genetic diversity of soybean (Glycine max (L.) Merr.) varieties and field bean (Glycine soza Sieb. and Zucc.) Five soybean varieties and one field bean were analysed with random primers using the polymerase chain reaction (PCR). Nine primers of a total twenty random primer were selected to amplify DNA segments. A total of 74 PCR products were amplified and 67.6% of which were polymorphic. The size of DNA molecule is ranged 0.13~2.0Kb and typically generated four to eight major bands. Specific genetic marker were revealed in primer sequence 5'-CAG GCC CIT C-3', 5'-TGC TCT GCC C-3' and 5'-GTC CAC ACG G-3', respectively. Genetic similarity between each of the varieties were calculated from the pair-wise comparisons of amplification products and a dendrogram was constructed by an unweighted pair-group method with arithmethical means (UPGMA). The results indicate that intervarietal relationships of soybean have a narrow genetic base and between the varieties, Hwanggum-kong and Seckryang-bootkong is more closely related than the rest of varieties, and field bean is related quite distant.

• Journal of Plant Biotechnology
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• v.43 no.1
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• pp.82-90
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• 2016

Most Araliaceae plant species distributed in Korea are economically important because of their high medicinal values. This study was conducted to develop barcode markers from sequence analysis of chloroplast DNA in 14 taxa of Araliaceae species grown in South Korea. Sequencing of seven chloroplast DNA regions was performed to establish the DNA barcode markers, as suggested by the Consortium for the Barcode of Life (CBOL). From the sequence analysis of chloroplast DNA, we identified specific sequences and nucleotides that allowed us to discriminate among each other 14 Korean Araliaceae species. The sequence in the region of psbA-trnH revealed the most frequent DNA indels and substitutions of all 7 regions studied. This psbA-trnH marker alone can discriminate among all 14 species. There are no differences between Korean and Chinese Panax ginseng in all seven sequenced chloroplast DNA regions. A phylogenetic tree constructed using the seven chloroplast DNA regions revealed that Tetrapanax papyriferus should be classified as an independent clade. The Aralia and Panax genera showed a close phylogenetic relationship. Five species in the Eleutherococcus genus were more closely related to Kalopanax septemlobus than to any Panax species.

• The Korea Journal of Herbology
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• v.36 no.1
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• pp.9-17
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• 2021

Objectives : Tetrapanacis Medulla and Akebiae Caulis are one of the most frequently adulterated herbal medicines because of their confusability of terms in the ancient writings and the similarity of morphological features of dried herbal products. The major adulterant is Aristolochia manshuriensis (Guanmutong) which has a serious safety concern with its toxicity. To ensure the safety and quality of the two herbal medicines, it is necessary to discriminate the toxic adulterant from authentic species. The aim of this study is to develop SCAR markers and to establish the multiplex-SCAR assay for discrimination of four plant species related to Tetrapanacis Medulla and Akebiae Caulis. Methods : ITS regions of fifteen samples of four species (Tetrapanax papyrifer, Fatsia japonica, Aristolochia manshuriensis, and Akebia quinata) collected from different sites were amplified and sequenced. Fifteen obtained ITS sequences were aligned and analysed for the detection of species-specific sequence variations. The SCAR markers were designed based on the sequence alignments and then, multiplex-SCAR assay enhancing rapidity was optimized. Results : ITS sequences clearly distinguished the four species at the species level. The developed SCAR markers and multiplex-SCAR assay were successfully discriminated four species and detected the adulteration of commercial product samples by comparison of the amplified DNA fragment sizes. Conclusions : These SCAR markers and multiplex-SCAR assay are a rapid, simple, and reliable method to identify the authentic Tetrapanacis Medulla and Akebiae Caulis from adulterants. These genetic tools will be useful to ensure the safety and to standardize the quality of the two herbal medicines.

• Journal of Korean Society of Forest Science
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• v.105 no.4
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• pp.422-428
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• 2016

Ginkgo (Ginkgo biloba L.) is one of the most appropriate roadside trees because of a good transplantation nature and ability to grow well in urban environment. Ginkgo is a dioecious species. Sex discrimination of ginkgo is possible through comparing morphological characters of reproductive organs. However, it needs more than about twenty years for reproductive organs to appear after sexual maturity. Until now, ginkgo trees for roadside plantation have been planted without discriminating the sex because ginkgo trees have been usually planted before sexual maturity. Ginkgo nuts from the female ginkgo trees planted along the roadside emit a foul odor, and make much pollution on the streets. Thus in this study a novel SCAR marker (SCAR-GBM) for the early sex discrimination was developed. Primers were developed on the basis of the sequence of male-specific RAPD variants reported previously. False-negative problem of SCAR marker, probably caused by dominant nature, was resolved by using multiplex PCR using primers of both the SCAR-GBM and a universal primer set of atp1 region in mitochondria DNA, which resulted in improved discrimination efficiency. The results showed that DNA bands of 1,039 bp were commonly amplified by the atp1 primer set in male and female trees, and SCAR-GBM markers of 675 bp were specifically amplified only in male trees. Reproducible and specific discrimination of the multiplex PCR was finally confirmed by applying multiple male and female individuals.

• Journal of Mushroom
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• v.7 no.4
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• pp.150-155
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• 2009

Because the import of Inonotus obliquus have been rapidly increased in Korea, we developed the Inonotus species-specific marker by using various sequences including ITS sequences, PCR-RFLP and STS primers and used this marker to determine both genetic relatedness and strains discrimination of Inonotus spp. Total 17 different Inonotus spp. were examined by using ITS sequences and classified into 2 different groups. One strain, ASI74008 isolated from Kamchaka island of Siberia, showed the high sequence identity (98%) at the nucleotide level to the other I. obliquus DSM strain, indicating the ASI74008 belong to I. obliquus species. Comparison of banding patterns after restriction enzyme digestions with PCR amplicons of ITS region revealed some variations depending on the species and strains. However, PCR products amplified with STS primer showed species specific patterns.Therefore, use of both STS primers and PCR-RFLP could help for better strain identification.

• Weed & Turfgrass Science
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• v.2 no.2
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• pp.191-197
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• 2013

Two medium-leaf ecotypes (CY6069, CY6097) belonging to one species (Zoysia japonica) of Korean lawngrasses were selected in sod production fields in Jang Seong, Korea. They were reported to have distinct morphological and growth rate characteristics different from the preferred medium-leaf type zoysiagrass in Korea. This study was conducted to define further the genotypic difference at the molecular level and to develop DNA marker based on the specific DNA fragment. Polymorphic DNA fragments were first explored by using randomly amplified polymorphic DNA (RAPD) primers, which were then converted into PCR-based sequence characterized amplified region (SCAR) markers. The CY6069-specific primer set amplified about 550 bp successfully, while the CY6097 marker produced the expected 690 bp band, by which those markers were nominated by CY6069_550 and CY6069_690 SCARs, respectively. Together with the reported morphological and other phenotypic features, the SCAR markers confirmed in this study will be useful to identify those medium-leaf zoysiagrass genotypes when they are cultivated with other vegetatively propagated warm-season turfgrasses in sod farms.

• Molecules and Cells
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• v.40 no.11
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• pp.828-836
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• 2017

Eukaryotic cells consist of a complex network of thousands of proteins present in different organelles where organelle-specific cellular processes occur. Identification of the subcellular localization of a protein is important for understanding its potential biochemical functions. In the post-genomic era, localization of unknown proteins is achieved using multiple tools including a fluorescent-tagged protein approach. Several fluorescent-tagged protein organelle markers have been introduced into dicot plants, but its use is still limited in monocot plants. Here, we generated a set of multicolored organelle markers (fluorescent-tagged proteins) based on well-established targeting sequences. We used a series of pGWBs binary vectors to ameliorate localization and co-localization experiments using monocot plants. We constructed different fluorescent-tagged markers to visualize rice cell organelles, i.e., nucleus, plastids, mitochondria, peroxisomes, golgi body, endoplasmic reticulum, plasma membrane, and tonoplast, with four different fluorescent proteins (FPs) (G3GFP, mRFP, YFP, and CFP). Visualization of FP-tagged markers in their respective compartments has been reported for dicot and monocot plants. The comparative localization of the nucleus marker with a nucleus localizing sequence, and the similar, characteristic morphology of mCherry-tagged Arabidopsis organelle markers and our generated organelle markers in onion cells, provide further evidence for the correct subcellular localization of the Oryza sativa (rice) organelle marker. The set of eight different rice organelle markers with four different FPs provides a valuable resource for determining the subcellular localization of newly identified proteins, conducting co-localization assays, and generating stable transgenic localization in monocot plants.

• Journal of Animal Science and Technology
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• v.52 no.6
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• pp.451-457
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• 2010

The porcine MHC (Major Histocompatibility Complex), encoding the SLA (Swine Leukocyte Antigen) genes, is one of the most significant regions associated with immune rejection in relation to transplantation. In this study, three SLA class I (SLA-1, SLA-3, SLA-2) loci and three SLA class II (DRB1, DQB1, DQA) loci were investigated in the previously unidentified Korean native pig (KNP) population that was closely inbred in the Livestock Technology Research Station in Cheongyang, Korea. Total thirteen KNPs from four generations were genotyped for the SLA alleles and haplotypes were investigated using PCR-SSP (Sequence-Specific Primer) method. The results showed that all of these KNPs had Lr-56.30/56.30 homozygous haplotype, indicating high level of inbreeding in the SLA genes. The inbreeding status of these animals was also investigated using microsatellite (MS) markers. From the 50 MS markers investigated, 17 MS markers were fixed in all generations and the fixed alleles are increased as 26 loci for the fourth generation. Two MS markers, S0069 and SW173, were heterozygous for all the animals tested. Observed and expected heterozygosities were calculated and the average inbreeding coefficients for each generation were also calculated. In the fourth generation, the average inbreeding coefficients was 0.732 and this may increase with further inbreeding process. Analysis of the SLA haplotypes and MS alleles can give important information for breeding the pigs for xenotransplantation studies.

• The Korean Journal of Mycology
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• v.38 no.1
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• pp.34-39
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• 2010

We have attempted to verify 30 strains of Hypsizigus marmoreus from various mushroom stocks in Korea using random amplified polymorphic DNA (RAPD) methodology. Chromosomal DNAs of them were extracted and subjected to PCR analyses with 3 random primers. Each PCR produced approximately 30 distinct PCR bands with the size from 200 bp to 3000 bp. A dendrogram was acquired using the unweighted pair-group method with arithmetic average (UPGMA) clustering methodology on the basis of the DNA band pattern. The analysis revealed that 30 strains of H. marmoreus were clustered into two distinct clusters. Cluster 1 contained 3 subgroups while the cluster 2 consisted of rather diverse strains. Interestingly, Hm3-10, a wild strain collected from Deog-Yu mountain, was not included in either clusters, indicative of uniqueness of this strain. We nextly attempted to develop strain-specific DNA markers to verify a specific strain. A unique band in the RAPD gel lane of Hm0-4 was extracted and its sequence was determined. PCR with a primer set from the determined sequence revealed that the primer set gave a 250 bp DNA band only for Hm0-4, indicating that this approach works well for the strain-specific identification of H. marmoreus.