• Title/Summary/Keyword: Bandsharing

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Genetic Differences within and between Populations of Korean Catfish (S. asotus) and Bullhead (P. fulvidraco) Analysed by RAPD-PCR

  • Yoon, Jong-Man;Kim, Jong-Yeon
    • Asian-Australasian Journal of Animal Sciences
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    • v.17 no.8
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    • pp.1053-1061
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    • 2004
  • Of the 20 arbitrarily chosen primers, six oligonucleotides decamer primers were used on the basis of the number of the polymorphisms generated in catfish (Silurus asotus) from Yesan and bullhead (Pseudobagrus fulvidraco) from Dangjin in Korea. Six primers were used generating a total of 602 scorable bands in catfish and 195 in bullhead population, respectively, ranging in size of DNA fragments from less than approximately 100 to larger than 2,000 base pairs (bp). Six primers yielded 199 polymorphic fragments (33.1%) in catfish and 47 (24%) in bullhead, respectively. In the present study, a total of 328 common fragments (an average of 54.7 per primer) were observed in catfish population, whereas 84 (an average of 14.0 per primer) in bullhead. The total number of specific fragments in catfish and bullhead population were 76 and 64, respectively. In catfish population, random decamer, OPA-17 (GACCGCTTGT) generated the highest number of fragments (a total of 141) in comparison with other primers used, with an average of 11.8. The common bands in the molecular weight of 300 bp generated by random primer OPA-06 (GGTCCCTGAC) were present in every individuals in bullhead population. The major polymorphic bands in the molecular weight of 100 bp generated by OPA-17 were identified in lane 14, 15, 17, 18, 19 20 and 21, which were identifying species in bullhead population. The average bandsharing values (BS values) of all of the samples within catfish population ranged from 0.575 to 0.945, whereas 0.063-1.000 within bullhead population. The bandsharing value (index of similarity between individuals) between individual No. 5 and No. 9 showed the highest level within catfish population, whereas the bandsharing value between individual No. 1 and No. 2 showed the lowest level. The single linkage cluster analysis resulted from four primers, indicating four genetic groupings composed of group 1 (C1-C10, all of the catfish samples), group 2 (B11, B12, B13, B14, B16, B17, B18, B19), group 3 (B15) and group 4 (B20 and B21). The dendrogram reveals close relationships between individual identities within two species populations and individuals derived from the same ancestor, respectively. However, genetic distances between two species populations ranged from 0.124 to 0.333. The shortest genetic distance (0.042) displaying significant molecular differences was between individual No. 6 and No. 9 catfish population. The shortest genetic distance (0.033) displaying significant molecular differences also was between individual No. 18 and No. 19 in bullhead population. Reversely, the genetic distance of individual No. 20/21 among individuals in bullhead population was highest (0.333). This result showed that bullhead No. 20 and 21 were distinct from other individuals within bullhead population.

Genetic Variation and Differences within and between Populations of Cultured and Wild Bullhead (Pseudobagrus fulvidraco) Revealed by RAPD-PCR

  • Yoon Jong-Man;Kim Gye-Woong;Park Hong-Yang
    • Reproductive and Developmental Biology
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    • v.29 no.4
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    • pp.213-221
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    • 2005
  • We used nine decamer primers to generate DNA fragment sizes ranging from 100 bp to 1,600 bp from two bullhead (Pseudobagrus fulvidraco) populations of Dangjin in Korea. 376 fragments were identified in the cultured bullhead population, and 454 in the population of wild bullhead from Dangjin: 287 specific fragments $(76.3\%)$ in the cultured bullhead population and 207 $(45.6\%)$ in the wild bullhead population. On average, a decamer primer was used to generate 34.2 amplified products in a cultured bullhead. A RAPD primer was used to generate an average of 3.1 amplified bands per sample, ranging between 2.5 and 6.0 fragments in this population. Nine primers also generated 24 polymorphic fragments (24/376 fragment, $6.4\%$) in the cultured bullhead population, and 24 (24/454 fragments, $5.2\%$) in the wild bullhead population. The OPA-16 primer, notably, produced which 11 out of 11 bands $(100\%)$ were monomorphic in the wild bullhead population. 110 intra-population-specific fragments, with an average of 12.2 per primer, were observed in the cultured bullhead population. 99 fragments, with an average of 11.0 per primer, were identified in the wild bullhead. Especially, 55 inter-population-common fragments, with an average of 6.1 per primer, were observed in the two bullhead populations. The bandsharing value (BS value) of individuals within the wild bullhead population was substantially higher than was determined in the cultured bullhead population. The average bandsharing value was $0.596\pm0.010$ within the cultured bullhead population,. and $0.657\pm0.010$ within the wild bullhead population. The dendrogram obtained with the nine primers indicates two genetic clusters, designated cluster $1\;(CULTURED\;01\~CULTURED\;11)$, and cluster $2\;(WILD\;12\~WILD\;22)$. Ultimately, the longest genetic distance displaying significant molecular differences was determined to exist between individuals in the two bullhead populations, namely between individuals WILD no. 19 of the wild bullhead population and CULTURED no. 03 of the cultured bullhead population (genetic distance = 0.714). RAPD-PCR allowed us to detect the existence of population discrimination and genetic variation in Korean population of bullhead. This finding indicates that this method constitutes a suitable tool for DNA comparison, both within and between individuals, populations, species, and genera.

Genetic distances of three venerid species identified by PCR analysis

  • Jeon, Jun-Hyub;Yoon, Jong-Man
    • The Korean Journal of Malacology
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    • v.31 no.4
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    • pp.257-262
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    • 2015
  • The seven selected primers BION-13, BION-29, BION-61, BION-64, BION-68, BION-72 and BION-80 generated the total number of loci, average number of loci per lane and specific loci in Meretrix lusoria (ML), Saxidomus purpuratus (SP) and Cyclina sinensis (CS) species. Here, the complexity of the banding patterns varied dramatically between the primers from the three venerid clam species. The higher fragment sizes (> 1,000 bp) are much more observed in the SP species. The primer BION-68 generated 21 unique loci to each species, which were ascertaining each species, approximately 150 bp, 300 bp and 450 bp, in the ML species. Remarkably, the primer BION-80 detected 7 shared loci by the three clam species, major and/or minor fragments of sizes 500 bp, which were matching in all samples. As regards average bandsharing value (BS) results, individuals from CS clam species (0.754) exhibited higher bandsharing values than did individuals from SP clam species (0.607) (P < 0.05). In this study, the dendrogram obtained by the seven oligonucleotides primers indicates three genetic clusters: cluster 1 (LUSORIA01-LUSORIA07), cluster 2 (PURPURATUS08-PURPURATUS14), cluster 3 (SINENSIS15-SINENSIS21). Among the twenty one venerid clams, the shortest genetic distance that displayed significant molecular differences was between individuals 18 and 20 from the CS species (genetic distance = 0.071), while the longest genetic distance among the twenty-one individuals that displayed significant molecular differences was between individuals LUSORIA no. 02 and PURPURATUS no. 09 (genetic distance = 0.778). Relatively, individuals of SP venerid species were appropriately closely related to that of CS species, as shown in the hierarchical dendrogram of genetic distances. Eventually, PCR fragments exposed in the present study may be worthwhile as a DNA marker the three venerid clam species to discriminate.

Genetic Differences of Three Pollicipes mitella Populations Identified by PCR Analysis

  • Song, Young-Jae;Yoon, Jong-Man
    • Development and Reproduction
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    • v.17 no.3
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    • pp.199-205
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    • 2013
  • Genomic DNAs were extracted from the turtle leg (Pollicipes mitella, 1798) population of Tongyeong, Yeosu and Manjaedo located in the southern sea of Korea. The turtle leg population from Tongyeong (0.929) exhibited higher bandsharing values than did turtle leg from Manjaedo (0.852). The higher fragment sizes (>1,200 bp) are much more observed in the Yeosu population. The number of unique loci to each population and number of shared loci by the three populations, generated by PCR using 7 primers in the turtle leg (P. mitella) population of Tongyeong, Yeosu and Manjaedo. Genetic distances among different individuals of the Tongyeong population of the turtle leg (lane 1-07), Yeosu population of the turtle leg (lane 08-14) and Manjaedo population of the turtle leg (lane 15-21), respectively, were generated using the CLASSIFICATION option in Systat version 10 according to the bandsharing values and similarity matrix. The dendrogram, obtained by the seven decamer primers, indicated three genetic clusters: cluster 1 (TONGYEONG 01 TONGYEONG 07), cluster 2 (YEOSU 08 YEOSU 14), and cluster 3 (MANJEDO 15 MANJEDO 21). Tongyeong population could be evidently discriminated with the other two Yeosu and Manjaedo populations among three populations. The longest genetic distance (0.305) was found to exist between individuals' no. 02 of the Tongyeong population and no. 13 of the Yeosu population. It seems to the authors that this is a result of a high degree of inbreeding in narrow region for a long while.

Genetic Variability between Ark Shell (Scapharca subcrenata, Lischke) Populations from Daecheon and Wonsan

  • Kim, Sun-Young;Kim, Jong-Yeon;Yoon, Jong-Man
    • The Korean Journal of Malacology
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    • v.25 no.1
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    • pp.5-13
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    • 2009
  • Genomic DNA isolated from two geographical ark shell (Scapharca subcrenata) populations was amplified several times by PCR reactions. The ark shell population from Daecheon (ASPD) and from Wonsan (ASPW) in the West Sea and the East Sea of Korean Peninsula, respectively, obtained. The seven arbitrarily selected primers OPA-05, OPA-11, OPB-09, OPB-11, OPB-14, OPC-18 and OPD-07 were shown to generate the loci observed per primer, shared loci by each population, specific loci, unique shared loci to each population and shared loci by the two populations which could be clearly scored. Here, 862 loci were identified in the ASPD population, and 1,191 in the ASPW population: 137 specific loci (15.9%) in the Daecheon population and 84 (7.1%) in the Wonsan population. 407 shared loci by each population, with an average of 58.1 per primer, were observed in the ASPD population. 473 shared loci by each population, with an average of 67.6 per primer, were identified in the ASPW population. The numbers of specific loci in the ASPD and ASPW population were 137 and 84, respectively. Consequently, the average bandsharing value of individuals within the ASPW population was much higher than in the ASPD population. The bandsharing value between individuals' no. 08 and no. 13 was 0.628, which was the highest measured between the two geographical populations. The dendrogram obtained by the seven primers indicated three genetic clusters: cluster 1 (DAECHEON 01-DAECHEON 11), cluster 2 (WONSAN 12 and 14) and cluster 3 (WON SAN 13, 15, 16, 17, 18, 19, 20, 21 and 22). The genetic distance between the two geographical populations ranged from 0.043 to 0.499. Especially, individual no. 10 of Daecheon population was most distantly related to no. 14 of Wonsan population (genetic distance = 0.499).

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Differences and Variations among Anguilla japonica, Muraenesox cinereus and Conger myriaster from the Yellow Sea

  • Yoon, Jong-Man
    • Development and Reproduction
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    • v.19 no.3
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    • pp.163-166
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    • 2015
  • Genomic DNAs were extracted from the muscle of twenty-one specimens of three eel species collected in Anguilla japonica (AJ), Muraenesox cinereus (MC) and Conger myriaster (CM) from the Yellow Sea, respectively. In the present study, 7 oligonucleotides primers generated 191 specific loci in the AJ species, 226 in the (MC) species and 181 in the CM species, respectively. The primer BION-02 generated the most loci (a total of 83), with an average of 11.86 in the AJ species. The specific loci generated by oligonucleotides primers exhibited inter-individual-specific characteristics, thus revealing DNA polymorphisms. With regard to average bandsharing value (BS) results, individuals from Conger myriaster species (0.808) exhibited higher bandsharing values than did individuals from Muraenesox cinereus species (0.729) (P<0.05). The longest genetic distance (0.430) displaying significant molecular difference was also between individual no. 01 within Anguilla japonica eel species and individual no. 04 within Anguilla japonica species. In this study, the dendrogram resulted from reliable seven oligonucleotides primers, indicating three genetic clusters composed of group I (ANGUILLA 01~ANGUILLA 07), group II (MURAENESOX 08~MURAENESOX 14) and group III (CONGER 15~CONGER 21). The existence of species differentiation and DNA polymorphisms among three eel species were detected by PCR analysis. As mentioned above, a dendrogram revealed close relationships between individual identities within three eel species. High levels of a significant genetic distance among three eel species showed this PCR approach is one of the most suitable tools for individuals and/or species biological DNA studies.

Genetic Distances of Crucian Carp Populations analyzed by PCR Approach

  • Jeon, Jun-Hyub;Yoon, Jong-Man
    • Development and Reproduction
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    • v.20 no.2
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    • pp.135-140
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    • 2016
  • Genomic DNAs isolated from crucian carp of four rivers, belonging to the family Cyprinidae was amplified by seven oligonucleotides primers. In the present study, we employed hierarchical clustering method in order to reveal genetic distances and variations. Crucian carp was acquired from Hangang river (CAH), Geumgang river (CAG), Nakdonggang river (CAN) and Yeongsangang river (CAY). The primer BION-12 generated the most loci (a total of 50) with an average of 10 in the CAY population. The primer BION-10 generated the least loci (a total of 19), with an average of 3.8 in the CAG population, in comparison to the other primers used. Seven oligonucleotides primers made 16.7 average no. per primer of specific loci in the CAH population, 7.4 in the CAG population, 8.6 in the CAN population and 0.9 in the CAY population, respectively. The specific loci generated by oligonucleotides primers revealed inter-individual-specific characteristics, thus disclosing DNA polymorphisms. The dendrogram obtained by the seven oligonucleotides primers indicates four genetic clusters. The genetic distance that displayed significant molecular differences was between individuals no.06 and no.08 from the CAG population (genetic distance = 0.036), while the genetic distance among the five individuals that displayed significant molecular differences was between individuals no.08 and no.09 from the CAG population (genetic distance = 0.088). With regard to average bandsharing value (BS) results, individuals from CAY population ($0.985{\pm}0.009$) exhibited higher bandsharing values than did individuals from CAH population ($0.779{\pm}0.049$) (P<0.05). Relatively, individuals of CAY population were fairly closely related to that of CAN location (genetic distance between two populations<0.016).

Genetic Distances of Three Mollusk Species Investigated by PCR Analysis

  • Oh, Hyun;Yoon, Jong-Man
    • Development and Reproduction
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    • v.18 no.1
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    • pp.43-49
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    • 2014
  • Three species of Nortamea concinua (NC) and Haliotis discus hannai (HDH) from Tongyeong and Sulculus diversicolor supertexta (SDS) are widely distributed on the coast of the Yellow Sea, southern sea and Jeju Island in the Korean Peninsula under the innate ecosystem. There is a need to understand the genetic traits and composition of three mollusk species in order to evaluate exactly the patent genetic effect. PCR analysis was performed on DNA samples extracted from a total of 21 individuals using seven decamer oligonucleotides primers. Seven primers were shown to generate the unique shared loci to each species and shared loci by the three species which could be clearly scored. A hierarchical clustering tree was constructed using similarity matrices to generate a dendrogram, which was facilitated by the Systat version 10. 236 specific loci, with an average of 56.3 per primer, were identified in the NC species. 142 specific loci, with an average of 44.7 per primer, were identified in the HDH species. Especially, 126 numbers of shared loci by the three species, with an average of 18 per primer, were observed among the three species. Especially, the decamer primer BION-75 generated 7 unique loci to each species, which were identifying each species, in 700 bp NC species. Interestingly, the primer BION-50detected 42 shared loci by the three species, major and/or minor fragments of sizes 100 bp and 150 bp, respectively, which were identical in all samples. As regards average bandsharing value (BS) results, individuals from HDH species (0.772) exhibited higher bandsharing values than did individuals from NC species (0.655). In this study, the dendrogram obtained by the seven decamer primers indicates three genetic clusters: cluster 1 (CONCINNA 01~CONCINNA 07), cluster 2 (HANNAI 08~HANNAI 14), cluster 3 (SUPERTEXTA 15~SUPERTEXTA 21). Comparatively, individuals of HDH species were fairly closely related to that of SDS species, as shown in the hierarchical dendrogram of genetic distances.

Genetic Variations of Three Tegillarca granosa Populations Investigated by PCR Technique

  • Yoon, Jong-Man
    • The Korean Journal of Malacology
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    • v.32 no.4
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    • pp.255-261
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    • 2016
  • The selected seven oligonucleotides primers BION-32, BION-33, BION-35, BION-38, BION-40, BION-46 and BION-58 generated the shared loci, specific loci, unique shared loci to each population and shared loci by the three T. granosa populations in Beolgyo, a Chinese site and Wonsan, respectively. The bandsharing value between individuals' no. 03 and no. 04 was 0.816, which was the highest value identified within the Beolgyo population. The primer BION-35 generated the most loci (a total of 70), with an average of 10.0 in the Wonsan population. On average, seven oligonucleotides primers generated 16.1 specific loci in the Beolgyo population, 22.3 in the Chinese population and 39.3 in the Wonsan population. 126 unique shared loci to each population, with an average of 18 per primer, were observed in the Beolgyo population, 63 loci, with an average of 9 per primer, were observed in the Chinese population, and 49 loci, with an average of 7 per primer, and were observed in the Wonsan population. The oligonucleotides primer BION-32 generated 14 unique loci to each population, which were identifying each population in the Beolgyo population. Interestingly, every primer had not distinguished the shared loci by the three populations, major and/or minor fragments of sizes, which were identical in almost all of the samples. As regards average bandsharing value (BS) results, individuals from Beolgyo population ($0.717{\pm}0.057$) exhibited higher BS values than did those from Wonsan population ($0.552{\pm}0.104$) (P < 0.05). The dendrogram resulted from truthful seven oligonucleotides primers, representing three genetic clusters comprising group I (BEOLGYO 01, 02, 03, 04, 05, 06 and 07), group II (CHINESE 08, 09, 10, 11, 12, 13 and 14) and group III (WONSAN 15, 16, 17, 18, 19, 20 and 21). In three T. granosa populations, the longest genetic distance (0.874) displaying significant molecular difference was also between individual no. 02 within the Beolgyo population and individual no. 12 within the Chinese population. Relatively, individuals of the CHINESE population were fairly closely related to those of the WONSAN population.

Geographic Variation in Pond Smelt (Hypomesus nipponensis) by RAPD Analysis (RAPD 분석에 의한 빙어 (Hypomesus nipponensis)의 지리적 변이)

  • Kim, Yong-Ho;Park, Su-Young;Yoon, Jong-Man
    • Korean Journal of Ichthyology
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    • v.18 no.1
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    • pp.1-11
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    • 2006
  • Genomic DNA isolated from two geographical populations of pond-smelt (Hypomesus nipponensis) was amplified for RAPD (randomly amplified polymorphic DNA) analysis. The populations were obtained from Chungju (CJ), in the inland area, and Dangjin (DJ), in the vicinity of the West Sea in Korea. Seven arbitrarily selected primers, OPB-06, OPB-10, OPB-13, OPB-17, OPC-09, OPC-17 and OPC-20, were used to generate the shared loci, polymorphic, and specific loci. Three hundred and eighty-three loci observed per primer were identified in the CJ population, and 287 were identified in the DJ population. Among them, 91 polymorphic loci or 23.8% were polymorphic in the CJ population, and 47 (16.4%) in the DJ population. The number of shared loci observed was 198 in the CJ population and 176 in the DJ population. Forty-four and 75 specific loci were detected in the CJ and DJ populations, respectively. Especially, 99 numbers of shared loci by the two populations, with an average of 14.1 per primer, were observed in the two pond-smelt populations. The average bandsharing value between the two geographical pond-smelt populations was $0.700{\pm}0.008$, ranging from 0.600 to 0.846. Compared separately, the bandsharing value of individuals within the CJ population was higher than that of the DJ population. The dendrogram obtained using the data from the seven primers indicated three genetic clusters: cluster 1, CJ 01, 02, 03, 04, 05, 06, 07, 08, 09, 10, and 11; cluster 2, DJ 01, 02, 03, 04, 05, 06, 07, 08, and 09; and cluster 3, DJ 10 and 11. The genetic distance between the two geographical populations ranged from 0.040 to 0.545. Thus, RAPD-PCR analysis revealed a significant genetic distance between the two pond-smelt populations.