RAPD와 URP를 이용한 심비디움 유전자원 유연관계 분석

박부희,김미선,이영란,박필만,이동수,예병우 한국화훼산업육성협회 2010 화훼연구 Vol.18 No.3

심비디움속 유전자원 48품종에 대하여 RAPD와 URP를 이용하여 유전적 유연관계를 분석하였다. RAPD분석에 는 10mer에 해당하는 random primer (Operon사) 80개 를, URP는 20 mer에 해당하는 12종의 상용 primer를 이 용하였다. 48 품종의 심비디움에는 34종의 동양 심비디움, 7종의 동서양란 교잡종, 7종의 서양 심비디움이 포함되어 있다. 선별된 41개의 random primer와 6개의 URP primer로부터 각각 407, 56개의 다형성 밴드를 획득 하여 총 463개의 마커를 이용하였다. 이들 마커의 크기 범위는 0.4 kb 에서 1.5 kb 에 해당하였다. 유전적 유사도 를 바탕으로 UPGMA clustering 프로그램을 이용하여 dendrogram을 작성하였는데 유전자원 48품종은 유사도 0.638 수준에서 총 4그룹으로 구분되었다. The genetic relationship among 48 Cymbidium cultivars was analyzed using randomly amplified polymorphic DNA (RAPD) with eighty 10 mers random primers (Operon Technologies) and twelve 20 mers random primers. Forty eight Cymbidium cultivars included 34 oriental Cymbidium, 7 hybrids, and 7 western Cymbidium. 407 (9.9 per primer) and 56 polymorphic bands (9.5 per primer) were generated by polymerase chain reaction with selected thirty 10 mers primers, and nine 20 mers primers, respectively. The polymorphic fragments ranged from 0.4 to 1.5 kb in size. The dendrogram was constructed by using the UPGMA clustering algorithm based on genetic similarity. Forty eight Cymbidium cultivars were classified into four major groups at similarity coefficient value of 0.638.

Genetic Distances in Two Gracilaria Species (Gracilariaceae, Rhodophyta) Identified by PCR Technique

Kim, Young Sik,Yoon, Jong-Man The Korean Society of Developmental Biology 2018 발생과 생식 Vol.22 No.4

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).

Genetic Distances in Two Gracilaria Species (Gracilariaceae, Rhodophyta) Identified by PCR Technique

Young Sik Kim,윤종만 한국발생생물학회 2018 발생과 생식 Vol.22 No.4

Genomic DNA was isolated from the Gracilaria vermiculophylla (GRV) and G. chorda (GRC) from Jang-heung located in the southern sea of the Korean Peninsula, respectively and we performed clustering analyses, DNA polymor-phisms 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±0.004 within GRV and 0.916±0.006 within GRC. The average BS value between two Gracilaria species was 0.340±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 individ-ual VERMICULOPHYLLA no. 07 of GRV was genetically closely related to VERMICULOPHYLLA no. 06 of GRV (genet-ic 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).

Taxonomic Review of the Genus Echinochloa in Korea (II): Inferred from Simple Sequence Repeats

이정란,김창석,이인용 한국잔디학회 2014 Weed & Turfgrass Science Vol.3 No.3

Echinochloa (L.) P. Beauv. includes some of the noxious weeds, causing a serious yield loss when they are dominantin the fields. Identification of the Echinochloa is very difficult because many interspecific and intraspecific forms of the species arefound. However, it is important to identify the species exactly and to know the genetic diversity of the species for effective weedmanagement. This study was conducted to identify and summarize the Echinochloa species by comparing the genetic variationand relationship among Korean Echinochloa species using SSR. The genetic diversity of 107 individuals, including seven specieswere assessed using five SSR markers. UPGMA dendrogram generated two clades (I and II) and clade II divided again into twosubclades (II-1 and II-2) whereas the model based genetic structure proposed four subpopulations. The two subpopulations werecorresponded to clades I and II-1 and the other two were arranged to clade II-2 of the UPGMA dendrogram. We have concludedthat E. colona and E. glabrescens might have not distributed in Korea. The biological varieties, praticola and echinata, of E. crus-gallishould be treated as E. crus-galli. Korean Echinochloa should be summarized with four species, i.e., E. oryzicola, E. crus-galli, E. esculenta, and E. oryzoides.

Genetic distances of three mollusk species determined by PCR analysis

Hyun Oh,Jong-Man Yoon 한국발생생물학회 2013 한국발생생물학회 학술발표대회 Vol.2013 No.8

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. Amplification products were separated by electrophoresis in 1.4% agarose gels (Bioneer Corp., Daejeon, Korea) with TBE (0.09 M Tris, pH 8.5; 0.09 M borate; 2.5 mM EDTA), using 100 bp DNA ladder (Bioneer Corp., Daejeon, Korea) as DNA molecular weight marker and detected by staining with ethidium bromide. Seven primers, BION-55 (5’-GTCACGGACG-3’), BION-50 (5’-CAAGCGA GGA-3’), BION-75 (5’-GAGGTCCACA-3’), BION-35 (5’-AGCGGCTAGG-3’), BION-61 (5’-GAC CGCTTGT-3’), BION-69 (5’-GCATCCACCA-3’) and BION-66 (5’-TGGTGGACCA-3’) 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 (SPSS Inc., Chicago, IL, USA). 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-50 detected 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 distances of four Manila clam (Ruditapes philippinarum) populations identified by PCR analysis

Jong-Man Yoon 한국발생생물학회 2017 한국발생생물학회 학술발표대회 Vol.2017 No.8

The author has investigated four Manila clam populations of the family Veneridae, belonging to the order Veneroida. The clam is also indigenous to some parts of the sandy regions of the West Sea in the Korean Peninsula, as well as in several areas in China. Clams are the most popular marine products in Korea because of their taste and nutritional value, and Koreans consume them in large quantities. However, in spite of their economic and scientific consequences, a little information currently exist regarding the physiological and ecological levels only of clam species in Korea. This study attempt is to elucidate the genetic distances within and between clam populations from the West Sea. Four populations of Manila clam (R. philippinarum) were obtained in adjacent district to the West Sea in Korea. Four populations of clam muscle was collected in sterile tubes, placed on ice immediately, and stored under refrigeration until needed. Genomic DNA was extracted and purified under the conditions described previously (Yoon and Kim, 2004). The degree of variability was calculated by use of the Dice coefficient (F), which is given by the formula: F=2 nab / (na+nb), where nab is the number of bands shared between the samples a and b, na is the total number of bands for sample a and nb is the total number of bands for sample b (Jeffreys and Morton, 1987; Yoke-Kqueen and Radu, 2006). Euclidean genetic distances within- and between-species were also calculated by complete linkage method with the support of the hierarchical dendrogram program Systat version 10. The genomic DNA isolated from four Manila clams populations in the West Sea, were amplified several times by PCR reaction. The dendrogram obtained by the six oligonucleotides primers indicates three genetic clusters. The hierarchical dendrogram indicates four main branches: cluster 1 (GOCHANG 01, 02, 04 and 05), cluster 2 (SEOCHEON 06, 07, 08, 09 and 10), cluster 3 (TAEAN 11, 12, 13, 14 and 15) and cluster 4 (ANMYEON 16, 17, 18, 19, 20 and GOCHANG 03). Multiple comparisons of average bandsharing values among Manila clam populations from four sections were generated according to the bandsharing values and similarity matrix. Ultimately, individuals from SEOCHEON clam population (0.637±0.227) exhibited higher bandsharing values than did individuals from GOCHANG clam population (0.402±0.115) (P<0.05).

Genetic Distances of Three Mollusk Species Investigated by PCR Analysis

Oh, Hyun,Yoon, Jong-Man The Korean Society of Developmental Biology 2014 발생과 생식 Vol.18 No.1

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 Distances of Three Mollusk Species Investigated by PCR Analysis

Hyun Oh,Jong-Man Yoon 한국발생생물학회 2014 발생과 생식 Vol.18 No.1

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 Distances of Three Mollusk Species Investigated by PCR Analysis

오현,윤종만 한국발생생물학회 2014 발생과 생식 Vol.18 No.1

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 Differences and Variation in Two Purple Washington Clam (Saxidomus purpuratus) Populations from South and North Korea

Yoon, Jong-Man,Park, Su-Young The Malacological Society of Korea 2006 The Korean Journal of Malacology Vol.22 No.2

Genomic DNA samples isolated from geographical purple Washington clam (Saxidomus purpuratus) were obtained from two different regions in Korean Peninsula: Gunsan (Gunsan population; GSP), and Haeju (Haeju population; HJP), a collection area in the vicinity of the West Sea. The seven arbitrarily primers, OPA-07, OPA-09, OPA-18, OPA-20, OPC-03, OPC-06 and OPC-09 were shown to generate the total loci, loci observed per primer, shared loci by each population, specific, and polymorphic loci which could be clearly scored. We also generated the unique shared loci to each population and shared loci by the two populations in purple Washington clam. The size of the DNA fragments also varied wildly, from 50 to 2,400 bp. Here, 304 total loci were identified in the GSP purple Washington clam population, and 282 in the HJP: 91 polymorphic loci (29.9%) in the GSP and 47 (16.7) in the HJP. 198 shared loci, with an average of 28.3 per primer, were observed in the GSP population. The decamer primer OPA-07 generated the shared loci by the two populations, approximately 1,000 bp, between the two Saxidomus populations. The oligonucleotide primer OPC-03 also generated the shared loci by the two populations, approximately 500 bp and 1,000 bp, in GSP population from Gunsan and HJP population from Haeju. The other primer, OPC-06 generated the shared loci by two Gomphina populations (approximately 400 bp). The dendrogram, generated by seven reliable primers, indicates three genetic clusters. The dendrogram obtained by the seven primers indicates three genetic clusters: cluster 1 (GUNSAN 01-GUNSAN 02), cluster 2 (GUNSAN 03-GUNSAN 11), and cluster 3 (HAEJU 12-HAEJU 22). The genetic distance between the two geographical populations ranged from 0.043 to 0.506. Especially, the longest genetic distance displaying significant molecular differences, 0.506, was found to exist between individuals GUNSAN no. 11 of Gunsan and HAEJU no. 17 of Haeju.