• Korean Journal of Agricultural Science
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• v.44 no.3
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• pp.318-324
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• 2017

With the development of next-generation sequencing (NGS), a cutting-edge technology, genotype-by-sequencing (GBS) became available at a low cost per sample. GBS makes it possible to customize the process of library preparation to obtain high-quality single nucleotide polymorphisms (SNPs) in the most efficient way. However, a GBS library is hard to construct due to fine-tuning of concentration of each reagent and set-up. The major reason for this is the presence of undigested genomic DNA (gDNA) owing to the efficiency of different restriction enzymes for different species with unknown reasons. Therefore, this proof-concept study is to demonstrate the unpredictable patterns of enzyme digestion from various plants in order to make the reader aware of the caution needed when choosing restriction enzymes for their GBS library preparations. Indeed, no pattern was found for the digestibility of gDNA samples and restriction enzymes in the current study. We suggest that more data should be accumulated on this matter to help researchers who want to apply GBS technologies in a variety of genetic approaches.

• Journal of the Korean Society of Food Science and Nutrition
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• v.27 no.6
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• pp.1160-1165
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• 1998

When total cellular DNA was isolated from Porphyra tenera by ultracentrifugation on Hoechst dye/CsCl gradients method, plasmid like DNA's were concentrated at the upper band which were characterized with a A＋T rich organelle DNA's in the CsCl gradients. Based on their electrophoretic migration in different concentration of agarose gel, buffer system, and electric power etc. and the results of restriction digestion, the plasmid like DNA's were concluded to have circular conformation. This is the first report of putative circular plasmid DNA from the P. tenera, which is a autonomously replicating plasmid existing with a high copy number plasmid in the cell. The minimum size of this plasmid estimated by restriction endonuclease digestion was appeared to be 2.5kb in size.

• Journal of Microbiology
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• v.41 no.4
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• pp.312-319
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• 2003

In an attempt to develop a method for rapid and accurate identification of six Vibrio species that are clinically important and most frequently detected in Korea, 16S rDNA restriction fragment length polymorphism (RFLP) of Vibrio type strains, as well as environmental isolates obtained from the Korean coastal area, was analyzed using ten restriction endonucleases. Digestion of the 16S rDNA fragments amplified by polymerase chain reaction (PCR) with the enzymes gave rise to 2~6 restriction patterns for each digestion for 47 Vibrio strains and isolates. An additional 2~3 restriction patterns were observed for five reference species, including Escherichia coli, Aeromonas hydrophila, A. salmonicida, Photobacterium phosphoreum, and Plesiomonas shigelloides. A genetic distance tree based on RFLP of the bacterial species correlated well with that based on 16S rDNA sequences. The very small 16S rDNA sequence difference (0.1%) between V. alginolyticus and V. parahaemolyticus was resolved clearly by RFLP with a genetic distance of more than 2%. RFLP variation within a species was also detected in the cases of V. parahaemolyticus, V. proteolyticus, and V. vulnificus. According to the RFLP analysis, six Vibrio and five reference species were assigned to 12 genotypes. Using three restriction endonucleases to analyze RFLP proved sufficient to identify the six pathogenic Vibrio species.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.9
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• pp.1226-1230
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• 2005

The present investigation was undertaken to study the genetic polymorphism of the DRB3 exon 2 in 75 crossbred cattle by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. Five genotypes i.e. HaeIII-a, HaeIII-b, HaeIII-e, HaeIII-ab and HaeIII-ae were observed when the 284 bp PCR products were digested with HaeIII restriction enzyme. The corresponding frequencies of these patterns were 0.53, 0.04, 0.01, 0.38 and 0.04, respectively. Digestion with RsaI restriction enzyme resolved 24 different restriction patterns. The frequencies of these patterns ranged from 0.013 (RsaI-f, RsaI-k and RsaI-c/n) to 0.120 (RsaI-n). The results revealed that the crossbred cows belonged to the RsaI patterns namely b, k, l, a/l, d/s, l/n, l/o and m/n, whose corresponding frequencies were 0.027, 0.013, 0.040, 0.027, 0.040, 0.067, 0.027 and 0.067, respectively. Digestion of the 284 bp PCR product of DRB3.2 gene with PstI in the crossbred cattle did not reveal any restriction site. These results suggested the absence of the recognition site in some of the animals. These results also revealed that the crossbred cows studied were in homozygous as well as heterozygous condition. On the basis of the above results it can be concluded that the DRB3.2 gene was found to be highly polymorphic in the crossbred cattle population.

• KSBB Journal
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• v.15 no.4
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• pp.411-413
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• 2000

A method is described for the rapid and simple isolation of genomic DNA from 3 mL culture of Lactobacillus crispatus KLB46 The isolated DNA using this method was shown to be an excellent substrate for restriction endonclease digestion and PCR. The method is expected to be used in gentic manipulation of L. crispatus KLB46.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.6
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• pp.752-756
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• 2011

Polymorphism of the second exon of the caprine leukocyte antigen-DRB3 gene (CLA-$DRB3^*02$) was investigated in this study. The 285 bp PCR product of 258 individuals from 10 domestic goat breeds in Southwest China was digested with restriction endonucleases PstI and HaeIII and then genotyped. Three alleles and 4 restriction digestion profiles were distinguished by digestion of the PCR fragment by PstI, and 8 alleles and 13 genotypes by HaeIII. For HaeIII restriction enzyme sites, the Chi-square ($X^2$) test showed that all goat breeds in this study did not fit with the Hardy-Weinberg equilibrium (p<0.01 or p<0.05). The highly polymorphic nature of CLA-$DRB3^*02$ was demonstrated and the ranges of gene heterozygosity (He) and polymorphism information content (PIC) were 0.36-0.63 and 0.32-0.55, respectively. Clustering analysis showed that the 10 goat breeds clustered into two groups and Dazu Black goat had a close genetic relationship with Chengdu Grey, Jintang Black and Nanjiang Yellow goats.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.2
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• pp.262-266
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• 2017

Objective: This study was conducted to screen scrotal hernia in domesticated swine from selected breeders in the Philippines. This defect is associated with a cytosine to thymine mutation in the BCL-2 associated X protein (BAX) gene of swine. Methods: Genetic screening was done by DNA extraction followed by amplification and digestion using polymerase chain reaction-restriction fragment length polymorphism, amplifying the 416 bp region of the BAX gene that was subjected to digestion using the Ear I enzyme. Sequencing was also conducted to validate the results. Results: Results revealed that out of 538 samples tested, 411 (76.4%) of the samples were found to be normal whereas the remaining were carriers of the mutation in which 80 (14.9%) were heterozygous mutants and 47 (8.7%) were homozygous mutants. Pietrain breed was found to have the highest incidence. Conclusion: Having a scrotal hernia eliminates the chances of using the boar as a breeder stock because the following generations arising from it would most likely exhibit herniation. It is therefore advised to establish a genetic screening method for Scrotal Hernia in the Philippines to eliminate the negative gene from the herd.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.30 no.1 s.244
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• pp.26-31
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• 2006

This paper reports low-cost PDMS/glass based DNA microbiochip for the restriction enzyme reaction and its products detection using the capillary electrophoresis. The microbiochip ($25mm{\times}75mm$) has the heater integrated reactor ($5{\mu}{\ell}$) for DNA restriction enzyme reaction at $37^{\circ}C$ and the microchannel ($80\;{\mu}m{\times}100\;{\mu}m{\times}58mm$) for the capillary electrophoresis detection. It is experimentally confirmed that the digestion of the plasmid ($pGEM^{(R)}-4Z$) by the enzyme (Hind III and Sca I) is performed for less than 10 min and its electrophoresis detection is able to sequentially on the fabricated microbiochip.

• Mycobiology
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• v.37 no.3
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• pp.240-242
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• 2009

An improved procedure for preparing PCR cloning vectors was developed. This procedure includes the incorporation of adapters to create XcmI restriction enzyme sites in pBluescript II SK(+) vectors, digestion with XcmI followed by further digestion of the small fragment produced by XcmI digestion with additional enzymes, and purification with PCR purification kits. Using this procedure, PCR cloning vectors with high ligation efficiencies and low blue or false-positive colonies were obtained.

• Journal of Ginseng Research
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• v.14 no.2
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• pp.310-316
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• 1990

This study was focused on the characterization of mitochondrial DNA (mtDNA) for molecular 9enetical approach of energy Production related mechanism in Panax ginseng. The simple and efficient method of mtDNA isolation from ginseng has been developed by modification of recently advanced methods. This procedure can successfully apply to mtDNA isolation of several plants. mtDNA of etiolated shoot and one-year root were digested with restriction endonucleases, but that of 6-year root not. Any difference was not observed in the restriction endonuclease digestion patterns among the ginseng variants. Molecular size of ginseng mtDNA was estimated at least 159 kb by the restriction endonuclease fragment analysis. The 4.5 kb extra band at the lane of EcoRII treatment could be observed in restriction patterns digested with the methylation sensitive endonucleases, BstN I and EcoRII. For construction of mitochondrial genomic library of ginseng, mtDNA was partially digested with EcoRl, and packaged with EMBL4 phage vector. Genomic library was screened and purified for further research including restriction mapping of ginseng mtDNA, and cloning of the genes. The gene of ATP synthase A subunit was cloned from the purified EMBL4 library clone No. 16. Now, clone No. 16 is subcloned for structure gene sequence analysis.