• Food Science of Animal Resources
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• v.27 no.2
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• pp.209-215
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• 2007

In order to develop a sensitive and reliable method for the species-specific molecular markers, PCR-RFLP assay of the mitochondrial DNA(mt DNA) 12S rRNA gene was exploited for the identification of the origin of animal meat species including cattle, pig, sheep, goat, horse, deer, chicken, duck and turkey. A specific primer pairs were designed, based on the nucleotide sequences of mt 12S rRNA gene, for the amplification of the highly conserved region in the gene of the animal species using PCR-RFLP technique. mt DNA was isolated from meat samples followed by DNA amplification using PCR with the specific primers. PCR amplification produced an approximately 455 bp fragment in each of these animal meats. To distinguish pleat species, the PCR amplicons were digested with restriction endonucleases Tsp5091 and MboI, respectively, which generates distinct RFLP profiles. The DNA profiles digested with Tsp5091 allowed the clear discrimination in the mammalian meat species and the DNA profiles digested with MboI in poultry meat species. Therefore, the PCR-RFLP profiles of mt 12S rRNA gene could be very useful to identify the origin of the raw materials in the raw meats as well as the processed meat products.

• Journal of Microbiology and Biotechnology
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• v.9 no.3
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• pp.334-339
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• 1999

More innovative molecular markers were investigated for rapid and consistent differentiation of Metarhizium anisopliae var. majus from M. anisopliae var. anisopliae. A total of 28 isolates were obtained from various countries and hosts: 13 isolates of M. anisopliae var. anisopliae, 12 isolates of M. anisopliae var. majus, and 3 isolates of M. anisopliae collected in Korea. This study involved restriction enzyme digestions of a PCR product amplified from nuclear internally transcribed spacer (ITS) and a portion of the 28S rDNA regions. Among 11 different restriction enzymes used in this study, MboⅠ digestion particularly produced a restriction pattern that had characteristics of M. anisopliae var. majus. This restriction pattern was consistent in all isolates of M. anisopliae var. majus regardless of their geographic origins and insect hosts. Mapping experiments revealed that MboⅠ sites of M. anisopliae var. majus are identical to those of M. anisopliae var. anisopliae with an exception for the presence of an additional site in the PCR product. Results from this study provide an additional method for identification and differentiation of isolates of these two varieties of M. anisopliae for use in the field and laboratory experiments.

• Journal of Genetic Medicine
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• v.7 no.1
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• pp.59-66
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• 2010

Purpose: Quantitative fluorescent polymerase chain reaction (QF-PCR) allows for the rapid prenatal diagnosis of common aneuploidies. The main advantages of this assay are its low cost, speed, and automation, allowing for large-scale application. However, despite these advantages, it is not a routine method for prenatal aneuploidy screening in Korea. Our objective in the present study was to validate the performance of QF-PCR using short tandem repeat (STR) markers in a Korean population as a means for rapid prenatal diagnosis. Material and Methods: A QF-PCR assay using an Elucigene kit (Gen-Probe, Abingdon, UK), containing 20 STR markers located on chromosomes 13, 18, 21, X and Y, was performed on 847 amniotic fluid (AF) samples for prenatal aneuploidy screening referred for prenatal aneuploidy screening from 2007 to 2009. The results were then compared to those obtained using conventional cytogenetic analysis. To evaluate the informativity of STR markers, the heterozygosity index of each marker was determined in all the samples. Results: Three autosomes (13, 18, and 21) and X and Y chromosome aneuploidies were detected in 19 cases (2.2%, 19/847) after QF-PCR analysis of the 847 AF samples. Their results are identical to those of conventional cytogenetic analysis, with 100% positive predictive value. However, after cytogenetic analysis, 7 cases (0.8%, 7/847) were found to have 5 balanced and 2 unbalanced chromosomal abnormalities that were not detected by QF-PCR. The STR markers had a slightly low heterozygosity index (average: 0.76) compared to those reported in Caucasians (average: 0.80). Submicroscopic duplication of D13S634 marker, which might be a unique finding in Koreans, was detected in 1.4% (12/847) of the samples in the present study. Conclusion: A QF-PCR assay for prenatal aneuploidy screening was validated in our institution and proved to be efficient and reliable. However, we suggest that each laboratory must perform an independent validation test for each STR marker in order to develop interpretation guidelines of the results and must integrate QF-PCR into the routine cytogenetic laboratory workflow.

• Journal of Life Science
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• v.15 no.3 s.70
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• pp.474-478
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• 2005

This study was conducted to analyze genetic characteristics and to develop the specific marker for Cheju native horse (Coo) at the level of sequence characterized amplified regions (SCARs). We collected blood samples from Cheju native horse and Thoroughbred horse (Th) and obtained genomic DNA from the blood of 50 individuals randomly selected within the breeds. Seven hundred primers were chosen randomly and were used to examin the polymorphism and 40 kinds of primers showed polymorphic RAPD band patterns between two breeds. Thirty primers of them showed horse specific bands. With the primer MG 30, amplified band of 2.0 kb showed the specificity to Cheju native horse (Cnh). Additionally MG 53 detected the thoroughbred horse (Th) specific markers at size of 2.3 kb. As the next, 2.3 kb band from MG 53 was checked with the all individuals from all the breeds of this study, and it maintained the reproducible breed specificity to thoroughbred horse (Th). With this results, 2.3 kb band was cloned into plasmid vector and sequenced bidirectionally from both ends of the cloned fragment. With the obtained sequences 10 nucleotide extended primers including the original arbitray primer were designed as a SCARs primer. Finally, the primer with extended sequence showed the reproducible breed differentiation pattern and it was possible to identify Cheju native horse (Cnh) from other breeds. The SCARs marker 2.3 kb from MG 53 could be used to identify Cheju native horse (Cnh) for not only registration but also horse breeding programe.

• Korean Journal of Breeding Science
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• v.42 no.2
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• pp.139-143
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• 2010

Late blight caused by Phytophthora infestans is historically a serious epidemic disease in potato and tomato cultivations. Accession L3708 (Solanum pimpinellifolium), a new source for late blight resistance was identified in AVRDC, and carries the resistance gene, Ph-3, incompatible to P. infestans race 3. The AFLP markers linked to Ph-3 were previously developed from the L3708 accession (Chunwongse et al. 2002). To facilitate tomato breeding with the Ph-3 gene, an attempt was made to convert AFLP markers to sequence-characterized amplified region (SCAR) markers. Among 6 AFLP markers, only one AFLP marker, L87, was successfully converted to SCAR marker. The resistance-specific 230 bp AFLP fragment was cloned and sequenced, and the PCR primer amplifying a 123 bp fragment was designed. This SCAR marker could discriminate resistant and susceptible individuals with high stringency. The developed SCAR marker could be used for the marker assisted-selection in tomato breeding programs.

• Korean Journal of Ecology and Environment
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• v.40 no.1
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• pp.143-148
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• 2007

The introduced exotic species has often caused severe problems to the native ecosystem. One of such species is the freshwater fish gengorobuna (Carassius cuvieri) introduced from Japan. The first step to assess harmful effects of this species on the Korean freshwater ecosystem is to discriminate it from the most similar native crucian carp (Carassius auratus). Because traditional morphological identification often gives unreliable results due to their highly similar phenotype, a new more efficient method is needed. For this purpose, molecular markers produced by the efficient one-step PCR method using three primers (DDF, DDR and DDR1) were developed and tested in the present study. This molecular marker will play an important role in monitoring fish community of Korean freshwater ecosystem.

• The Korea Journal of Herbology
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• v.39 no.2
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• pp.1-9
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• 2024

Objectives : Paeng-hwal is described as an insect herbal medicine used for digestive diseases in the Dong-ui-bo-gam. The origin of this herbal medicine is limited to several small crabs, such as Helice tridens. These crab species cohabitat in the same environment and share similar morphological characteristics, making it very difficult to distinguish and collect the individual species for use in dietary supplements or herbal medicines. This study was conducted to develop a genetic identification tool for discriminating among these closely related small crab species. Methods : CO1 DNA barcode regions of 15 samples from 6 species of small crabs were analyzed to obtain the individual sequences. To identify the correct species, comparative analyses were carried out using the database of the NCBI GenBank and the NIBR. SCAR primers were designed to develop simple and rapid assay methods using inter-species specific sequences. Optimal SCAR assay conditions were established through gradient PCR, and the limit of detection (LOD) was determined. Results : Six species of small crabs (Helicana tridens, Macrophthalmus abbreviatus, Helicana tientsinensis, Helicana wuana, Chiromantes dehaani, and Hemigrapsus penicillatus), which are distributed as Paeng-hwal, were identified through CO1 sequences analysis. We also developed SCAR markers to distinguish between six small crabs at the species level. Furthermore, we established the optimal PCR assay methods and the LOD of each individual species. Conclusions : The rapid and simple SCAR-PCR assay methods were developed to identify the species and control the quality of herbal medicines for Paeng-hwal based on the genetic analyses of CO1 DNA barcodes.

• Journal of Korean Society of Forest Science
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• v.108 no.3
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• pp.302-310
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• 2019

Precise and fast identification of crop cultivars is essential for efficient breeding and plant breeders' rights. Traditional methods for identification of jujube cultivars are based on the evaluation of morphological characteristics. However, due to time constraints and environmental influences, it is difficult to distinguish cultivars using only morphological traits. In this study, we cloned fragments from improved inter simple sequence repeats (ISSR) analysis, and developed stably diagnostic sequence-characterized amplified region (SCAR) markers. The specific ISSR bands of jujube cultivars from Dalizao and Boeundaechu were purified, cloned, and sequenced. As a result, four clones labeled 827Dalizao550, 827Boeun750, 846Boeun700, and 847Dalizao850 were identified. In order to investigate whether they were specific for the jujube cultivar, four pairs of SCAR primers were then designed and polymerase chain reaction (PCR) amplifications were conducted to analyze 32 samples, including jujube and sour jujube. In the PCR amplification of the 827Dalizao550 SCAR marker, the specific bands with 550 bp were amplified in six samples (Dalizao, Sandonglizao, Dongzao, Yuanlin No. 2, Suanzao 2, Suanzao 4), but unexpected bands (490 bp) were amplified in the others. Moreover, in the PCR amplification of the 847Dalizao850 SCAR marker, the specific bands with 850 bp were found in three samples (Dalizao, Sandonglizao, and Dongzao) and 900 bp unexpected bands were amplified in five samples (Pozao, Suanzao 1, Suanzao 2, Suanzao 3, Suanzao 4). These results showed that newly developed markers could be useful as a fast and reliable tool to identify jujube cultivars. However, further identification of polymorphic information and the development of SCAR markers are required for the identification of more diverse cultivars.

• Journal of Animal Science and Technology
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• v.45 no.4
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• pp.523-528
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• 2003

This study was performed to investigate a possible association of the porcine estrogen receptor(ER) locus with the total number of born(TNB) and number of born alive(NBA) in Yorkshire pigs. Using DNAs extracted from 242 Yorkshire pigs, the ER genotype was determined by PvuII PCR-RFLP. The ER allele frequencies of two types of A and B were 0.39 and 0.61, respectively. The least squares means of the litter size by ER genotype was evaluated. The TNB and NBA were found to be associated with an specific ER allele. The genotype at the porcine ER locus has an application potential for marker-assisted selection for litter size in pigs.

• Korean Journal of Plant Resources
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• v.9 no.3
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• pp.305-310
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• 1996

Five edible mountain vegetables(Saussurea sp. Aster tataricus, A. scaber. Synurus deltoides, Ligularia fischeri) were investigated on the basis of amplified DNA polymorphisms resulted from PCR (polymerase chain reaction) analysis. The sampled plants consisted of 38 individuals in 5 taxa. Only 10 primers out of 62 primers (60 random [10-mer] primers, two 15-mer [M13 core sequence, and (GGAT) sequence]) tested gave rise to polymorphisms in all of the tested plants, producing 176 DAN fragments amplified. Intraspecific polymorphisms found in each taxa showed intraspecies constancy (31.1-61.1%) in the banding patterns of individual plants: Saussurea sp. 31.1%, 15 bands, Aster tataricus, 40.9%, 18 bands, A. scaber. 38.5%, 15 bands. Synurus deltoides, 34.7%, 17 bands, and Ligularia fischeri, 61.1%, 22 brands, respectively. All five species were well classified from each other at the 0.93 level of similarity index value. Intraspecific and interspecific variations were appeared at the levels ranging from 0.62 to 0.99. Based on these results, our PCR analyses support the previous data derived from external morphology of the 5 edible mountain vegetables, but very low levels o intraspecific variations were detected in all of these taxa.