• 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.

• Korean Journal of Ecology and Environment
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• v.43 no.2
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• pp.271-278
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• 2010

Field monitoring was conducted for fish fauna and community assessment at 7 sites from April 2008 to October 2009 in the Chogang Stream. The number of fish samples in this period were 4,669 in 36 species of 9 families. Family Cyprinidae take 66.7 (24 species), Cobitidae, Bagridae, Centropomidae and Odontobutidae occupied 5.6%(each 2 species), respectively. Twenty species (55.6%) including Acheilognathus koreensis and A. yamatsutae were found endemic out of the 36 species. The species of Pseudopungtungia nigra, Gobiobotia macrocephala and Gobiobotia brevibarba were endangered species. The most frequently found one was Zacco koreanus (34.0%, n=1,588) followed by Z. platypus (22.6%, n=1,053) and Coreoleuciscus splendidus (13.3%, n=623). The lower reach of Chogang Stream was more abundance of species, high diversity, evenness and richness, and lower dominance index than those of the upper reach. According to the dendrogram established at 0.5 level of similarity rate, sampling stations were divided into 3 groups. They were divided into upper most stream (St. 1~St. 2), upper stream (St. 3), middle and lower stream (St. 4~St. 7). Overall, it was concluded that the Chogang Stream has been relatively well protected from the anthropogenic disturbance for the legally protected species including the endemic species studied in this study.

• Journal of Life Science
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• v.20 no.1
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• pp.119-123
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• 2010

Genetic variations of Chajogi (Perilla frutescens var. crispa) germplasms were investigated by using RAPD markers. Twenty-two Perilla frutescens var. crispa lines collected from various locations were subjected to RAPD analysis using 80 primers. Among them, only 22 primers showed polymorphic bands and these 22 primers provided a total of 224 bands consisting of 127 polymorphic and 97 monomorphioc bands. The polymorphic bands were subjected to phylogenetic analysis using the UPGMA method. From UPGMA, similarity co-efficiency of 22 Chajogi lines ranged from 0.72 to 0.94. The dendrogram of 22 lines obtained through the UPGMA method resulted in two groups (one major group and one minor group). Although the two groups were roughly consistent with growth phenotypes (period of flowering, period of maturity, stem length, number of branches, number of nodes, number of flower clusters and number of ovaries) in detail, much inconsistency also was present

• The Korean Journal of Mycology
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• v.35 no.2
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• pp.61-67
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• 2007

Twelve URP primers were used to assess genetic characteristics of oyster mushroom including 59 Pleurotsu ostreatus cultivars, two of P. florida cultivars, one P. sajor-caju cultivars, one P. abalonus cultivar and two P. eryngii cultivars registered in Korea. Six URP primers produced PCR polymorphic bands within and between the Pleurotus species. Primer URP2F produced distinct cultivar specific PCR polymorphic bands that profiled to 15 cultivar types. PCR polymorphic bands amplified by URP2F, URP6R, URP4R and URP2R were used for UPGMA cluster analysis. Fifty nine cultivars of Pleurotus ostreatus are genetically clustered into 5 groups, showing genetic similarity over 70% among them and P. abalonus. P. eryngii and P. sajor-caju, were involved in outside groups.

• The Korean Journal of Mycology
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• v.42 no.2
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• pp.159-164
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• 2014

For development of a method for differentiation of Pleurotus eryngii cultivars, simple sequence repeats (SSR) from whole genomic DNA sequence analysis was used for genotyping and two multiplex-SSR primer sets were developed. These SSR primer sets were employed to distinguish 12 cultivars and strains. Five polymorphic markers were selected based on the genotyping results. PCR using each primer produced one to four distinct bands ranging in size from 200 to 300 bp. Polymorphism information content (PIC) values of the five markers were in the range of 0.6627 to 0.6848 with an average of 0.6775. Unweighted pairgroup method with arithmetic mean clustering analysis based on genetic distances using five SSR markers classified 12 cultivars into two clusters. Cluster I and II were comprised of four and eight cultivars, respectively. Two multiplex sets, Multi-1 (SSR312 and SSR366) and Multi-2 (SSR178 and SSR277) completely discriminated 12 cultivars and strains with 21 alleles and a PIC value of 0.9090. These results might be useful in providing an efficient method for the identification of P. eryngii cultivars with separate PCR reactions.

• Korean Journal of Plant Resources
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• v.26 no.4
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• pp.491-502
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• 2013

Persimmon (Diospyros kaki Thunb) fruit is one of the most important fruit and have been cultivated from ancient times in Korea. In this study, we found 16 EST-SSR markers that contained one or more EST-SSR sites from 246 cDNA sequences. The developing of EST-SSR marker analysis from 42 persimmon cultivars was compared by genetic relationships and morphological relationships using 6 qualitative traits (fruit related 6 traits) and 19 quantitative traits (flower related 19 traits). In this study, 25 primer sets were tested to identify PCR polymorphism and 14 potential EST-SSR primer pairs were selected. The result of morphological relationship EST-SSR marker analysis showed that the coefficient 0.02 was difficult to categorize in several groups. And then, coefficient 0.77 of genetic relationship showed that the group was classified as four groups. The result of correlation distance between genetic relationship and morphological relationship were investigated was low significance (-0.03). Our results also provided an optimized method for improvement of breeding efficiency and introduce of superior character at persimmon cultivars using EST-SSR markers which was useful for further investigation.

• Korean Journal of Microbiology
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• v.41 no.1
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• pp.60-66
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• 2005

To select the rapid and efficient molecular subtyping method for epidemiologic monitoring of Staphylococcus aureus (S. aureus) strains at clinical laboratory levels, a total 116 of S. aureus and MRSA (methicillin-resistant S. aureus) strains from diverse animal species [Korean cattle, goat, pig, dog, chicken, mouse] and also humans were analyzed. To evaluate the discriminatory ability (DA) of individual PCR methods, random amplified polymorphic of DNA [RAPD; 4M & RA primer], repetitive extragenic palindromic sequences PCR (REP-PCR), and enterobacterial repetitive intergenic consensus sequences PCR (ERIC-PCR) methods were conducted and then compared on their Simpson's index of diversity (SID) values based on the dendrogram patterns, which was produced by software program (BiolD2+ & GelCompar II). In first, RAPD using the 4M primer (SID 0.915) was expressed more higher SID value than that of RA primer (SID 0.874). 4M primer was expressed more powerful DA than RA. Both REP-PCR (SID 0.930) and ERIC-PCR (SID 0.929) methods showed much more higher DA than that of RAPD. According to the present results, both REP-PCR and ERIC-PCR among the tested analysis methods were found as the most reliable and discriminative molecular subtyping method, because they expressed the highest DA for the present S. aureus and MRSA strains.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.29 no.3
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• pp.320-331
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• 1996

Electrophoretic comparisons of 482 individuals of Todarodes pacificus from 9 fishing areas were made to estimate genetic variability and differentiation using 17 enzymes. Strong activities were shown by 9 enzymes with 11 gene loci. The 9 sample lots could be divided into 3 genetic groups, based on dendrogram analysis using the Nei's genetic distance. The Summer, Autumn and Winter cohorts were identified as three seperated ecological populations which maintain genetic exchange. It is postulated that either the Summer cohort or the Autumn cohort has indepenently developed a local population that was isolated by hydrographic factors.

• Fisheries and Aquatic Sciences
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• v.8 no.3
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• pp.151-160
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• 2005

Genomic DNA samples isolated from Fenneropenaeus chinensis (fleshy prawn; FP) and Palaemon gravieri (Chinese ditch prawn; CDP) collected in the West Sea, off the Korean Peninsula, at Buan, were PCR-amplified repeatedly. The sizes of the DNA fragments generated by seven different primers varied from 50 bp to 1,600 bp. We identified 358 fragments for the FP species and 301 fragments for the CDP species. There were 18 polymorphic fragments (5.03$\%$) for the FP species and 12 (3.99$\%$) for the CDP species. In total, 66 common fragments (average of 9.4 fragments per primer) were observed for the FP species and 44 fragments (average of 6.3 fragments per primer) were observed for the CDP species. The numbers of specific fragments seen for the FP species and CDP species were 38 and 47, respectively. The complexity of the banding patterns varied dramatically between the primers and the two species. In the FP species, a specific fragment of approximately 1,200 bp generated by primer OPB-04 exhibited inter-individual-specific characteristics that were indicative of DNA polymorphisms. Moreover, in the CDP species, a major fragment of approximately 550 bp generated by primer OPB-20 was found to be specific for the CDP. The average bandsharing value between the two prawn species was 0.421$\pm$0.006, and ranged from 0.230 to 0.611. The dendrogram obtained using the data from the seven primers indicated seven genetic clusters: cluster 1, FLESHY 01, 02, 03, and 04; cluster 2, FLESHY 05, 06, and 07; cluster 3, FLESHY 08, 09, 10, and 11; cluster 4, DITCH 13, 14, 16, and 18; cluster 5, DITCH 12, 15, and 17; cluster 6, DITCH 19, 20, and 21; and cluster 7, DITCH 22. The genetic distance between the two prawn species ranged from 0.071 to 0.642. Thus, RAPD-PCR analysis revealed a significant genetic distance between the two prawn species. Using various arbitrary primers, RAPD-PCR may be applied to identify specific/polymorphic markers that are particular to a species and geographic population, and to define genetic diversity, polymorphisms, and similarities among shrimp species.

• Journal of Korea Port Economic Association
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• v.30 no.4
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• pp.151-168
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• 2014

The purpose of this paper is to show the brief efficiency and clustering measurement way by using the game cross-efficiency model which is newly introduced in this paper for 13 container ports during 3 years(2009, 2010, and 2013) with 3 input variables(depth, total area, and number of crane) and 1 output variable(container TEU). The main empirical results are as follows. First, the average rankings of game cross-efficiency model are Ningbo, Hongkong, Shanghai, Dubai, Singapore, Qingdao, Kaosiung, Busan, Tokyo, Incheon, Nagoya, Manila, Gwangyang ports in order. Second, according to ANOVA analysis, three models show the similar results in terms of the efficiency rankings. Third, in the clustering analysis using dendrogram, group A(Shangahi and Busan), group B(Ningbo and Nagoya), and group C(Incheon and Manila) show the common clustering ports during 3 or 2 years. The policy implication of this paper is that Korean port policy planner should introduce the game cross-efficiency method when measuring the individual port efficiency. Also port authority should consider the merits of the clustering ports for improving the port management and operations.