• Journal of fish pathology
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• v.19 no.2
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• pp.141-153
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• 2006

Genomic DNA samples isolated from two geographical crayfish (Cambaroides similis) populations in the inland of the Korean Peninsula, at Jeonju (Jeonju crayfish; JJC) and Jeongup (Jeongup crayfish; JUe), were PCR-amplified repeatedly. The six arbitrarily selected primers OPC-03, OPC-06, OPC-09, URP-02, URP07 and URP-09 generated the common, specific, and polymorphic fragments. The sizes of DNA fragments also varied widely, from 100 bp - 2,600 bp. Here, 521 fragments were identified in the JJC population, and 354 in the JUC population: 6 primers generated 60 specific fragments (60/521 fragment, 11.5%) in the JJC population, and 90 (90/354 fragments, 25.4%) in the JUC population. These primers produced 42 polymorphic fragments (8.1%) in the DC population, and 18 (5.1%) in the mc population. Especially these results demonstrate that the primers detected numerous specific fragments. Especially, the decamer primer OPC-06 generated inter-population-common DNA fragments, approximately 400 and 800 bp, respectively, in both the JJC and JUC populations. The universal primer URP-02 also generated inter-population-identical DNA fragments, approximately 350 bp and 600 bp, between the two geographical crayfish populations. Based on the average bandsharing values of all samples, the bandsharing value of individuals within the JJC population was much higher than in the JUC population. The bandsharing value between individuals no. 10 and no. 15 was 0.683, which was the highest between the two geographical populations. The dendrogram obtained by the six primers indicates two genetic clusters: cluster I (CRAYFISH 01 - CRAYFISH II), and cluster 2 (CRAYFISH 12 - CRAYFISH 22). The genetic distance between the two geographical populations ranged from 0.053 to 0.605. Ultimately, the longest genetic distance displaying significant molecular differences was found to exist between individuals in the two crayfish populations, between individuals CRAYFISH no. 02 of Jeonju and CRAYFTSH no. 15 of Jeongup (genetic distance = 0.605).

• Journal of Aquaculture
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• v.19 no.2
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• pp.67-76
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• 2006

Genomic DNA isolated from two Porphyra species, P. tenera and P. dentate from Wando located on the southern coast of Korean peninsula was amplified by PCR reaction. The amplified products were separated by agarose gel electrophoresis (AGE) with decamer primer and stained with ethidium bromide. The eight arbitrarily selected primers OPA-04, OPA-06, OPB-01, OPB-08, OPB-10, OPB-11, OPB-14 and OPC-10 generated the shared loci, polymorphic, and specific loci. The size of DNA bands varies from 100 bp to 2,200 bp. The complexity of the banding patterns varies dramatically between the primers and two Porphyra species. A total of 528 loci observed were identified in P. tenera and 443 in P. dentata: 22 polymorphic loci (4.2%) in P. tenera and 30 (6.8%) in P. dentata. 154 shared loci observed, the average 19.3 per primer, were identified in P. tenera and 143 loci, the aver-age 17.9 per primer, in P. dentata species. The number of specific loci in P. tenera and P. dentata was 73 and 77, respectively. The average bandsharing value was $0.623{\pm}0.008$ with P. tenera and $0.560{\pm}0.009$ within P. dentata. The average bandsharing value between two Porphyra species was $0.408{\pm}0.004$, ranged from 0.305 to 0.564. The dendrogram obtained by the eight primers indicates four genetic clusters. The genetic distance between two Porphyra species ranged from 0.076 to 0.627. The individual no. 02 of P. tenera was genetically closely related to no. 01 of P. tenera(genetic distance=0.082). Especially, two entities between the individual DENTATA no.21 and DENTATA no. 19 of P. dentata showed the longest genetic distance (0.627) in comparison with other individuals used. In this study, RAPD-PCR analysis has revealed the significant genetic distance between two Porphyra species pairs (P<0.001).

• Development and Reproduction
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• v.20 no.4
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• pp.379-385
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• 2016

Seven oligonucleotides primers were shown to generate the shared loci, specific loci, unique shared loci to each species and shared loci by the three species which could be obviously scored. In the present study, 7 oligonucleotides primers produced 401 total loci in the Styela clava (SC) species, 390 in the Halocynthia roretzi (HR) and 434 in the Styela plicata (SP), respectively. Seven oligonucleotides primers generated 275 specific loci in the SC, 341 in the HR and 364 in the SP species, respectively. The oligonucleotides primer BION-23 generated 28 unique loci to each species in the SP species. Especially, the oligonucleotides primer BION-25 produced 7 unique loci to each species, which were identifying each species in the SP species. BION-17 distinguished 21 shared loci by the three ascidian species, major and/or minor fragments of sizes, which were identical in almost all of the samples. Based on the average bandsharing values of all samples, the similarity matrix ranged from 0.519 to 0.774 in the SC species, from 0.261 to 0.683 in the HR species and from 0.346 to 0.730 in the SP species. As regards average bandsharing value (BS) results, individuals from SC species ($0.661{\pm}0.081$) exhibited higher bandsharing values than did individuals from HR species ($0.555{\pm}0.074$) (P<0.05). The dendrogram obtained by the seven oligonucleotides primers indicates three genetic groups. In three ascidian species, the shortest genetic distance (0.071) exhibiting significant molecular difference was also between individual no. 20 and no. 21 within the SP species.

• Development and Reproduction
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• v.5 no.2
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• pp.151-158
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• 2001

Genomic DNA from the blood of crucian carp(Carassius carassiu) from lake and aquaculture facility in Kunsan, Korea was extracted in order to identify genetic differences by polymerase chain reaction-randomly amplified polymorphic DNAs(PCR-RAPD). Out of 12 primers, 6 generated 266 highly reproducible RAPD markers, producing approximately 2.1 polymorphic bands per primer in crucian carp from lake. The degree of similarity varied from 0.18 to 0.76 as calculated by bandsharing analysis in crucian carp from lake. The RAPD outlines obtained with DNA of two different crucian carp populations from Kunsan were different(0.47 from lake and 0.70 from aquaculture facility, respectively). The electrophoretic analysis of polymerase chain reaction-randomly amplified polymorphic DNAs(PCR-RAPD) products showed high levels of similarity between different individuals in crucian carp from aquaculture facility. This result implies the genetic similarity due to raising in the same environmental condition or inbreeding within the crucian carp from aquaculture facility in Kunsan. In other words, crucian carp may have high levels of genome DNA diversity due to the introduction of the wild population from the other sites of Knsan even if it may be the geographical diverse distribution of this species. Generally, the RAPD polymorphism generated by these primers may be useful as a genetic marker for strain or population identification of important aquacultural fish species, crucian carp. However, in future, additional populations and sampling sites will be necessary to complement weak points.

• Development and Reproduction
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• v.16 no.4
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• pp.315-320
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• 2012

The gDNA isolated from Cyclina sinensis from Gochang (GOCHANG), Incheon (INCHEON) and a Chinese site (CHINESE), were amplified by PCR. Here, the seven oligonucleotide decamer primers (BION-66, BION-68, BION-72, BION-73, BION-74, BION-76, and BION-80) were used to generate the unique shared loci to each population and shared loci by the three cyclina clam populations. As regards multiple comparisons of average bandsharing value results, cyclina clam population from Chinese (0.763) exhibited higher bandsharing values than did clam from Incheon (0.681). In this study, the dendrogram obtained by the seven decamer primers indicates three genetic clusters: cluster 1 (GOCHANG 01~GOCHANG 07), cluster 2 (INCHEON 08~INCHEON 14), cluster 3 (CHINESE 15~CHINESE 21). The shortest genetic distance that displayed significant molecular differences was between individuals 15 and 17 from the Chinese cyclina clam (0.049), while the longest genetic distance among the twenty-one cyclina clams that displayed significant molecular differences was between individuals GOCHANG no. 03 and INCHEON no. 12 (0.575). Individuals of Incheon cyclina clam population was somewhat closely related to that of Chinese cyclina clam population. In conclusion, our PCR analysis revealed a significant genetic distance among the three cyclina clam populations.

• Development and Reproduction
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• v.22 no.3
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• pp.283-288
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• 2018

The author carried out PCR-based genetic platform to investigate the hierarchical polar dendrogram of Euclidean genetic distances of one bastard halibut population, particularly for Paralichthys olivaceus, which was further connected with those of the other fish population, by involving with the precisely designed oligonucleotide primer sets. Eight oligonucleotides primers were used generating excessively alterating fragments, ranging in size of DNA bands from larger than approximately 100 bp to less than 2,000 bp. As regards average bandsharing value (BS) results, individuals from Hampyeong population (0.810) displayed lower bandsharing values than did individuals from Wando population (0.877). The genetic distance between individuals approved the existence of close relationship in the cluster II. Relatively, individuals of one bastard halibut population were fairly related to that of the other fish population, as shown in the polar hierarchical dendrogram of Euclidean genetic distances. The points of a noteworthy genetic distance between two P. olivaceus populations demonstrated this PCR procedure is one of the quite a few means for individuals and/or populations biological DNA investigates, for species security and proliferation of bastard halibut individuals in coastal region of the Korea.

• Development and Reproduction
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• v.22 no.4
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• pp.393-402
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• 2018

Genomic DNA was isolated from the Gracilaria vermiculophylla (GRV) and G. chorda (GRC) from Jangheung located in the southern sea of the Korean Peninsula, respectively and we performed clustering analyses, DNA polymorphisms and the genetic differences. The seven selected primers OPC-01, OPA-04, OPA-05, OPD-07, OPD-08, OPB-10, and OPD-16 generated average bandsharing (BS) value, the genetic distance and dendrogram. The size of DNA bands varies from 90 bp to 2,400 bp. The average BS value was $0.859{\pm}0.004$ within GRV and $0.916{\pm}0.006$ within GRC. The average BS value between two Gracilaria species was $0.340{\pm}0.003$, ranged from 0.250 to 0.415. The dendrogram obtained by the seven primers, indicates two genetic clusters. The genetic distance between two Gracilaria species ranged from 0.059 to 0.513. The individual VERMICULOPHYLLA no. 07 of GRV was genetically closely related to VERMICULOPHYLLA no. 06 of GRV (genetic distance=0.059). Especially, two entities between the individual VERMICULOPHYLLA no. 10 of GRV and CHORDA no. 22 of GRC showed the longest genetic distance (0.513) in comparison with other individuals used. Accordingly, as mentioned above, PCR analysis showed that the GRV was a little more genetically diverse than the GRC species. We convinced that this DNA analysis revealed a significant genetic distance between two Gracilaria species pairs (p<0.01).

• Korean Journal of Ichthyology
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• v.17 no.3
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• pp.173-186
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• 2005

Genomic DNA was isolated from two geographic populations of largehead hairtail (Trichiurus lepturus) in Korea and the Atlantic Ocean. The eight arbitrarily selected primers were found to generate common, polymorphic, and specific fragments. The complexity of the banding patterns varied dramatically between primers from the two locations. The size of the DNA fragments also varied widely, from 150 bp (base pairs) to 3,000 bp. Here, 947 fragments were identified in the largehead hairtail population from Korea, and 642 in the largehead hairtail population from the Atlantic Ocean: 148 specific fragments (15.6%) in the Korean population, and 61 (9.5%) in the Atlantic population. In the Korean population, 638 common fragments with an average of 79.8 per primer were observed.; 429 common fragments, with an average of 53.6 per primer, were identified in the Atlantic population. The number of polymorphic fragments in the largehead hairtail population from Korea and the Atlantic Ocean was 76 and 27, respectively. Based on the average bandsharing values of all samples, the similarity matrix ranged from 0.784 to 0.922 in the Korean population, and from 0.833 to 0.990 in the Atlantic population. The bandsharing value of individuals within the Atlantic population was much higher than in the Korean population. The dendrogram obtained by the eight primers indicated two genetic clusters: cluster 1 (KOREAN 01~KOREAN 11), and cluster 2 (ATLANTIC 12~ATLANTIC 22). Individual KOREAN no. 10 from Korea was genetically most closely related to KOREAN no. 11 in the Korean population (genetic distance = 0.038). Ultimately, individual KOREAN no. 01 of the Korean population was most distantly related to ATLANTIC no. 16 of the Atlantic population (genetic distance = 0.708).

• Journal of Aquaculture
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• v.17 no.1
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• pp.69-80
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• 2004

The objective of the present study was to analyze genetic distances, variation and characteristics of individuals in rainbow trout, Oncorhynchus mykis using amplified fragment length polymorphism (AFLP) method as molecular genetic technique, to detect AFLP band patterns as genetic markers, and to compare the efficiency of agarosegel electrophoresis (AGE) and polyacrylamide gel electrophoresis (PAGE), respectively. Using 9 primer combinations, a total of 141 AFLP bands were produced, 108 bands (82.4%) of which were polymorphic in AGE. In PAGE, a total of 288 bands were detected, and 220 bands (76.4%) were polymorphic. The AFLP fingerprints of AGE were different from those of PAGE. Separation of the fragments with low molecular weight and genetic polymorphisms revealed a distinct pattern in the two gel systems. In the present study, the average bandsharing values of the individuals between two populations apart from the geographic sites in Kangwon-do ranged from 0.084 to 0.738 of AGE and PAGE. The bandsharing values between individuals No.9 and No. 10 showed the highest level within population, whereas the bandsharing values between individuals No.5 and No.7 showed the lowest level. As calculated by bandsharing analysis, an average of genetic difference (mean$\pm$SD) of individuals was approximately 0.590$\pm$0.125 in this population. In AGE, the single linkage dendrogram resulted from two primers (M11+H11 and M13+H11), indicating six genetic groupings composed of group 1 (No.9 and 10), group 2 (No. 1, 4, 5, 7, 10, 11, 16 and 17), group 3 (No. 2, 3, 6, 8, 12, 15 and 16), group 4 (No.9, 14 and 17), group 5 (No. 13, 19, 20 and 21) and group 6 (No. 23). In AGE, the genetic distances among individuals of between-population ranged from 0.108 to 0.392. In AGE, the shortest genetic distance (0.108) displaying significant molecular differences was between individuals No.9 and No. 10. Especially, the genetic distance between individuals No. 23 and the remnants among individuals within population was highest (0.392). Additionally, in the cluster analysis using the PAGE data, the single linkage dendrogram resulted from two primers (M12+H13 and M11+H13), indicating seven genetic groupings composed of group 1 (No. 15), group 2 (No. 14), group 3 (No. 11 and 12), group 4 (No.5, 6, 7, 8, 10 and 13), group 5 (No.1, 2, 3 and 4), group 6 (No.9) and group 7 (No. 16). By comparison with the individuals in PAGE, genetic distance between No. 10 and No. 7 showed the shortest value (0.071), also between No. 16 and No. 14 showed the highest value (0.242). As with the PAGE analysis, genetic differences were certainly apparent with 13 of 16 individuals showing greater than 80% AFLP-based similarity to their closest neighbor. The three individuals (No. 14, No. 15 and No. 16) of rainbow trout between two populations apart from the geographic sites in Kangwon-do formed distinct genetic distances as compared with other individuals. These results indicated that AFLP markers of this fish could be used as genetic information such as species identification, genetic relationship or analysis of genome structure, and selection aids for genetic improvement of economically important traits in fish species.

• Korean Journal of Animal Reproduction
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• v.23 no.4
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• pp.303-311
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• 1999

Nuclear DNA was isolated from the sperm cells representing genetic characteristics and genomic polymorphisms of rainbow trout by polymerase chain reaction(PCR) amplification of DNA using arbitrary primers. Genomic DNA fingerprints were generated from rainbow trout sperm DNA by polymerase chain reaction amplification using 20 arbitrary decamers as primers. Out of these primers, 4 generated 17 highly reproducible RAPD markers, producing almost six polymorphic bands per primers. Four of 6 primers tested generated amplified fragments which were polymorphic between different individuals. Polymorphic DNA fragments were reproducibly amplified from independent DNA preparations made from individuals. Rainbow trout was distinctly observed 3 specific DNA markers (2. 3, 2.0 and 1.3kb) in bandsharing. Individual fragments generated using the same arbitrary primer, demonstrated that a single primer detected at least three independent genomic polymorphisms in rainbow trout sperm DNA. The RAPD polymorphism generated by this primer may be used as a genetic marker for individual identification The RAPD-PCR technique has been shown to reveal informative polymorphism in many species of fish. The present results demonstrate that RAPD markers are abundant, reproducible and provide a basis for future gene mapping and MAS in these important aquaculture species using RAPD polymorphic markers. It is concluded that RAPD polymorphisms are useful as genetic markers for fish breed differentiation.