• Journal of the Korean Data and Information Science Society
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• v.25 no.5
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• pp.999-1009
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• 2014

Hierarchical clustering analysis helps easily exploring massive microarray data and understanding biological phenomena with dendrogram. But, because hierarchical clustering algorithms only consider the absolute similarity, it is difficult to illustrate a relative dissimilarity, which consider not only the distance between a pair of clusters, but also how distant are they from the rest of the clusters. In this study, we introduced the relative hierarchical clustering method proposed by Mollineda and Vidal (2000) and compared hierarchical clustering method and relative hierarchical method using the simulated data and the real data in the various situations. The evaluation of the quality of two hierarchical methods was performed using percentage of incorrectly grouped points (PIGP), homogeneity and separation.

• Development and Reproduction
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• v.14 no.3
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• pp.163-170
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• 2010

The gDNA isolated from Korean cuttle fish (Sepia esculenta Hoyle) from Sockcho (SOCKCHO), Seocheon (SEOCHEON), Incheon (INCHEON) and Vietnamese cuttle fish (VIETNAM), were amplified by PCR. Here, the seven selected primers (BION-A07, BION-A09, BION-A11, BION-A20, BION-B04, BION-B06, and BION-B14) were used to generate the unique shared loci to each population and shared loci by the four cuttle fish populations. In this study, the primer BION-A11 detected 112 shared loci by the four populations, major and/or minor fragments of sizes 300 bp, 400 bp, 700 bp and 1,000 bp, respectively, which were identical in all samples. The dendrogram obtained by the seven primers indicates five genetic clusters: cluster 1 (SOCKCHO 01-SOCKCHO 07), cluster 2 (SEOCHEON 08-SEOCHEON 10), cluster 3 (SEOCHEON 11-SEOCHEON 14), cluster 4 (INCHEON 15-INCHEON 21), and cluster 5 (VIETNAM 22-VIETNAM 28). The shortest genetic distance that displayed significant molecular differences was between individuals 25 and 26 from the Vietnamese cuttle fish (0.025), while the longest genetic distance among the twenty-eight cuttle fishes that displayed significant molecular differences was between individuals SOCKCHO no. 02 and SEOCHEON no. 12 (0.640). Individual of Seocheon and Incheon cuttle populations was somewhat closely related to that of Vietnamese cuttle fish population. Even though it could not be affirmed by a single case, such a result seems to be closely connected that the Korean peninsula is subject to climate changes by global warming. In conclusion, our PCR analyses revealed a significant genetic distance among the four cuttle fish populations.

• Journal of Sericultural and Entomological Science
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• v.44 no.2
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• pp.59-63
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• 2002

Phylogenetic relationships among mulberry varieties (Morus species) were analyzed on the basis of RAPD in order to identify the possibility of classification for the species. Polymorphisms under RAPD method were compared among 41 mulberry varieties. From the results of RAPD for 41 mulberry varieties by use of 30 different primers, 151 polymorphic bands were formed out of 201 ones. Under the dendrogram based on cluster analysis with the polymorphic bands, the varieties were classified into 7 groups including two large and five small ones on 0.747 value of genetic similarity coefficient. In the large groups 19 and 16 varieties were belong to group I and III, respectively. On the other hand, relatively high genetic similarity was shown among the varieties belonging to the group I, II and III. While, relatively low similarity were done between them in the group IV-Ⅵ and the other groups, and Mohusang in the group Ⅶ showed the lowest phylogenetic relationship with the other varieties.

• Journal of Plant Biotechnology
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• v.47 no.1
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• pp.15-25
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• 2020

Allium L. is one of the largest genera of the Amaryllidaceae family, with more than 920 species including many economically important species used as vegetables, spices, medicines, or ornamental plants. Currently, DNA barcoding tools are being successfully used for the molecular taxonomy of Allium. A total of 46 Allium species were collected from their native areas, and DNA was extracted using the IBRC DNA extraction kit. We used specific primers to PCR amplify matK. DNA sequences were edited and aligned for homology, and a phylogenetic tree was constructed using the neighbor-joining method. The results show thymine (38.5%) was the most frequent and guanine (13.9%) the least frequent nucleotide. The matK regions of the populations were quite highly conserved, and the amount of C and CT was calculated at 0.162 and 0.26, respectively. Analysis of the nucleotide substitution showed C-T (26.22%) and A-G (8.08%) to have the highest and lowest percent, respectively. The natural selection process dN/dS was 1.16, and the naturality test results were -1.5 for Tajima's D and -1.19 for Fu's Fs. The NJ dendrogram generated three distinct clades: the first contained Allium austroiranicum and A. ampeloprasum; the second contained A. iranshahrii, A. bisotunense, and A. cf assadi; and the third contained A. rubellum and other species. In this study, we tested the utility of the matK region as a DNA barcode for discriminating Allium. species.

• Horticultural Science & Technology
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• v.18 no.2
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• pp.103-106
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• 2000

The genetic relationship of Bletilla striata native to Korea and Japan was investigated using random amplified polymorphic DNA (RAPD). The 156 reproducible DNA bands, consisted of 58 polymorphic and 98 monomorphic bands, were obtained by polymerase chain reaction (PCR) with selected 10 random primers. The 8 Bletilla lines have been classified into three groups according to the similarity coefficient obtained by RAPD analysis. The dendrogram showed overall correlationship between similarity coefficient of 0.48 and 0.84. The first group included A (Bletilla striata native to Korea), B (Bletilla striata variegated and native to Korea in Mokpo), C (Bletilla striata variegated and native to Korea), D and E (Bletilla striata native to Japan). In this group, it was showed that B and C had the most similar genetic relationship. The similarity coefficient between D and E was 0.77. D and E had a very close resemblance in plant height and flower color with A native to Korea, respectively. The second group included only G (dwarf Bletilla native to Japan) and had a different morphological character compared to other cultivars. The last group included F and H (dwarf and variegated Bletilla native to Japan) and they had a similarity of variegation.

• Korean Journal of Plant Resources
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• v.13 no.2
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• pp.104-110
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• 2000

To analyse the genetic relationship and intraspecific variations among the Eleutherococcus senticosus population, the polymerase chain reaction(PCR) was performed total genomic DNAs of 10 E. senticosus collections by random 10 primers. The genetic diversity and genetic distance among 10 collections of Eleutherococcus spp. were used to describe the dendrogram showing phylogenic relationship. Ten collections were classfied into two group(group I, II) at the similarity coefficient value of 0.50. Group I included E. senticosus of Bukhado(Japanese), youngwal(Korea), E. seoulense, and E. chiisanesis while group II included several internal and Russia collection. The range of polymorphism was from 66.7 to 90.9% in 87 amplified DNA fragments. The similarity value of all collections ranged from 0.41 to 0.92. The average of genetic distance was 0.61.

• Korean Journal of Breeding Science
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• v.43 no.5
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• pp.399-404
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• 2011

Genetic diversity among 28 Cymbidium varieties was evaluated by using a sequence-related amplified polymorphism (SRAP) marker system. The SRAP marker which was based on the open reading frames (ORFs) regions was developed primarily for Brassica species, but has been applied to various crops. A total of 30 SRAP primer combinations were initially screened. Twenty-eight SRAP primer combinations showed high polymorphism among the 28 Cymbidium varieties, which were consisted of breeding varieties and their parents in National Institute of Horticultural & Herbal Science (NIHHS). The amplified DNA fragments were separated by denaturing acrylamide gels and detected silver staining method. One hundred ninety six polymorphic bands (7 per primer) were generated and ranged from 0.3 to 1.0 kb in size. Polymorphic fragments were scored for calculating simple matching coefficient of genetic similarity and cluster analysis with multi-variate statistical package (MVSP) 3.1. The mean genetic similarity coefficient value was 0.588. The results showed that the correlation between $F_1$ varieties and their parents was high. These studied SRAP markers will be useful tools for genotype identification, germplasm conservation, genetic relationships in Cymbidium.

• Fisheries and Aquatic Sciences
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• v.22 no.6
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• pp.12.1-12.8
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• 2019

Background: Wild fish populations stock is continuously diminishing in the Indo-Ganges river basin, and the population status of most fishes is unidentified. The identification of the population status and the conservation of commercially important and endemic wild fish populations in this region are crucial for the management. The aim of this paper was to identify the population status of Cirrhinus reba, a promising aquaculture but vulnerable species in the Indo-Ganges river basin in Bangladesh. Methods: C. reba samples were collected from four isolated populations of the Brahmaputra (n = 30), the Padma (33), the Karatoya (31), and the Jamuna Rivers (30) in Bangladesh, and the population status was evaluated using morphometric and landmark comparisons. Data were analyzed with the Kruskal-Wallis test, univariate analysis, discriminant function analysis, and the formation of a dendrogram. Results: Three meristic characters (Pectoral fin rays, caudal fin rays, scale in lateral lines), four morphometric characters (head length, pre-orbital length, post-orbital length, maximum body depth), and truss measurement (4-7) were significantly different among the stocks. The step-wise discriminant function analysis retained 15 variables from morphometric and landmark measurements that significantly differentiated the populations based on the constructed DFI and DFII. Discriminate function analysis also showed that 91.2% of the original groups were classified into their correct samples. The cluster analysis of Euclidean distances placed the Jamuna population in one cluster and the Brahmaputra, the Padma, and the Karatoya populations in the second one. Conclusion : Morphological differences among the stock were probably due to different ancestral origin. This is the first report about population status of C. reba in their natural habitat of the Indian subcontinent. Further genetic studies and the evaluation of environmental impact on C. reba populations in Bangladesh are suggested to support our findings.

• Horticulture, Environment, and Biotechnology : HEB
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• v.59 no.6
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• pp.875-888
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• 2018

Tulip (Tulipa L.) is one of the most important ornamental geophytes in the world. Analysis of molecular variability of tulips is of great importance in conservation and parental lines selection in breeding programs. Of the 70 genic microsatellites, 15 highly polymorphic and reproducible markers were used to assess the genetic diversity, structure, and relationships among 280 individuals of 36 wild and cultivated tulip accessions from two countries: Iran and the Netherlands. The mean values of gene diversity and polymorphism information content were 0.69 and 0.66, respectively, which indicated the high discriminatory power of markers. The calculated genetic diversity parameters were found to be the highest in wild T. systola Stapf (Derak region). Bayesian model-based STRU CTU RE analysis detected five gene pools for 36 germplasms which corresponded with morphological observations and traditional classifications. Based on analysis of molecular variance, to conserve wild genetic resources in some geographical locations, sampling should be performed from distant locations to achieve high diversity. The unweighted pair group method with arithmetic mean dendrogram and principal component analysis plot indicated that among wild tulips, T. systola and T. micheliana Hoog exhibited the closest relationships with cultivated tulips. Thus, it can be assumed that wild tulips from Iran and perhaps other Middle East countries played a role in the origin of T. gesneriana, which is likely a tulip species hybrid of unclear origin. In conclusion, due to the high genetic variability of wild tulips, they can be used in tulip breeding programs as a source of useful alleles related to resistance against stresses.

• Korean Journal of Plant Resources
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• v.31 no.6
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• pp.641-651
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• 2018

Floral scents and metabolites from cut flowers of 14 peony cultivars (Paeonia lactiflora Pall.) were analyzed to discriminate different cultivars and to compare the Korean cultivar with the other cut peonies imported to Korea using electronic nose (E-nose) and Fourier transform infrared (FT-IR) spectroscopy combined with multivariate analysis, respectively. Principal component analysis (PCA) and discriminant function analysis (DFA) dendrogram of peony floral scents were not precisely same but there were 3 groups including same cultivars. PCA and partial least squares-discriminant analysis (PLS-DA) dendrograms of peony metabolites showed that different cut peony cultivars were clustered into two major groups including same cultivars. Fragrance pattern of Korean 'Taebaek' was classified to same group with 'Jubilee' on the PCA and DFA results and its metabolite pattern was clearly discriminated by the PCA and PLS-DA compared to the other cultivars. These results show that the 14 peony cut flowers could be discriminated corresponding to their chemical relationship and the metabolic profile of Korean 'Taebaek' has distinctive characteristics. Furthermore, we suggest that these results could be used as the preliminary data for breeding new cut peony cultivars and for improving the availability of Korean cut peony in cosmetic industry.