• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2004.04a
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• pp.273-276
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• 2004

Genome-scale expression data provides us with valuable insights about organisms, but the biological validation of in-silico analysis is difficult and often controversial. Here we present a new approach for integrating previously established knowledge with computational analysis. Based on the known biological evidences, IGAM (Integrated Gene Association Matrix) automatically estimates the relatedness between a pair of genes. We combined this association knowledge to the regulatory network modeling and fuzzy clustering in yeast 5. Cerevisiae. The result was found to be more effective for extracting biological meanings from in-silico inferences for gene expression data.

• The Plant Pathology Journal
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• v.19 no.5
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• pp.221-226
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• 2003

Twenty universal rice primers (URPs) were used to detect PCR polymorphisms in 25 isolates of six different Alternaria species producing host specific toxins (HST). Eight URPs could be used to reveal PCR polymorphisms of Alternaria isolates at the intra- and inter-species levels. Specific URP-PCR polymorphic bands that are different from those of the other Alternaria spp. were observed on A. gaisen and A. longipes isolates. Unweighted pair-group method with arithmetic mean (UPGMA) cluster analysis using 94 URP polymorphic bands revealed three clustered groups (A. gaisen group, A. mati complex group, and A. logipes group).

• Korean Journal of Veterinary Research
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• v.45 no.2
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• pp.199-205
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• 2005

DNA fingerprint patterns of 8 Brucella reference strains and 15 B. abortus field isolates were characterized by repetitive element sequence-based PCR (rep-PCR) using BOX- and ERIC-primers in this study. AMOS PCR differentiated all Brucella field isolates from B. abortus RB51, a vaccine strain by producing a B. abortus-specific 498 bp band. Rep-PCR using BOX-primer produced 13 to 18 bands with sizes of between 230 and 3,300 bp, and discriminated Brucella strains to the species level except B. canis and B. suis. PCR products amplified with ERIC primers were, however, not appropriate for differentiating the Brucella isolates. DNA fingerprint patterns for all B. abortus field isolates were identical among them and were put on one cluster with B. abortus biovar 1 reference strain in the dendrogram, indicating they were highly clonal. These results suggested that rep-PCR using BOX primer might to be a useful tool for calculating genetic relatedness among the Brucella species and for the study of brucellosis epidemiology.

• Horticultural Science & Technology
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• v.33 no.5
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• pp.737-750
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• 2015

This study was carried out to construct a DNA profile database for 102 watermelon cultivars through the comparison of polymorphism level and genetic relatedness using genomic microsatellite (gMS) and expressed sequence tag (EST)-microsatellite (eMS) markers. Sixteen gMS and 10 eMS primers showed hyper-variability and were able to represent the genetic variation within 102 watermelon cultivars. With gMS markers, an average of 3.63 alleles per marker were detected with a polymorphism information content (PIC) value of 0.479, whereas with eMS markers, the average number of alleles per marker was 2.50 and the PIC value was 0.425, indicating that eMS detects a lower polymorphism level compared to gMS. Cluster analysis and Jaccard's genetic distance coefficients using the unweighted pair group method with arithmetic average (UPGMA) based on the gMS, eMS, and combined data sets showed that 102 commercial watermelon cultivars could be categorized into 6 to 8 major groups corresponding to phenotypic traits. Moreover, this method was sufficient to identify 78 out of 102 cultivars. Correlation analysis with Mantel tests for those clusters using 3 data sets showed high correlation ($r{\geq}0.80$). Therefore, the microsatellite markers used in this study may serve as a useful tool for germplasm evaluation, genetic purity assessment, and fingerprinting of watermelon cultivars.

• Journal of Mushroom
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• v.8 no.1
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• pp.27-32
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• 2010

This study was carried out to analyze the genetic relationships among 22 strains of Sparassis crispa, which were collected from various regions of worldwide. The cleaved amplified polymorphic sequence were obtained from the ribosomal DNA ITS regions of each strain. Based on the sequence analysis, the presence of five different groups were observed. Most strains shared the high nucleotide sequence similarity (about 90%) to each other, except only one strain, KACC50866. Nucleotide sequence similarity of KACC50866 was below 10% to other strains, indicating the genetic relatedness of strain KACC50866 was low compared to other strains. More works such as mitochondria genome analysis should help to determine the precise genetic diversity of S. crispa strains.

• Korean Journal of Veterinary Research
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• v.38 no.1
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• pp.53-63
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• 1998

Total of 1085 swine sera (1996-1997) from nation-wide were tested for the presence of antibodies to influenza A virus. Fifty nine percent of the tested sera showed seropositive by HI test. Positive sera consisted of 24--- of H3, 15--- of H1, and 20--- of the sample had both antibodies, respectively. Sera collected from various region represented 7~27--- seropositivity to H1N1, 15~25--- to H3N2, respectively. Swine influenza field isolate from nasal swab was characterized antigenically and genetically to elucidate its relatedness with other known strains of influenza A virus. The study was focused on the HA gene which is related to pathogenecity and antigenic variability of the influenza virus. By RT-PCR using influenza A/H1N1 specific primers, influenza virus H1N1 specific DNA fragment was amplified from A/Swine/Iowa/15/30(H1N1), US field isolate but not in H3N2 strain. PCR products were sequenced by dideoxy chain termination method to determine nucleotide homology with other strains of influenza A virus. The US field isolate and A/Swine/Indiana/1726/88 strain had 97--- of nucleotide homology and 98--- of amino acid homology. Based on the results obtained from this experiment, the field isolate was genetically related to A/Swine/Indiana/1726/88 and had higher homology with A/Swine/Indiana/1726/88 than with classical swine influenza virus, A/Swine/Iowa/15/30. The field isolate had no amino acid changes at the antigenic site compare to that of the A/Swine/Indiana/1726/88. The proteolytic enzyme cleavage site between HA1 and HA2 had no alteration and the amino acid arginine was intact. There is no evidence has been found that the field isolate has genetic shift or genetic drift which might altered antigenic determinant.

• Journal of fish pathology
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• v.34 no.2
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• pp.141-147
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• 2021

In this study, of the imported shrimps between 2017 and 2020, we investigated white spot syndrome virus (WSSV), covert mortality nodavirus (CMNV) and decapod iridescent virus 1 (DIV-1). Of the imported shrimps (a total of 29 groups), WSSV was detected as 31% (9/29) by nested PCR assay. And CMNV and DIV-1 were not identified in this study. To investigate the genetic relatedness of WSSV identified from imported shrimp, VR 14/15 region showed WSSV genomic variable loci was compared with reference isolates. Among the nine WSSV-positive samples, VR 14/15 region was amplified in only a sample (20-CH-1 isolate, imported from China in 2020). And the 20-CH-1 isolate showed 99.8% identity with WSSV-IN-05-01 which was reported in India in 2005, suggesting that those of WSSV have been spread from India to China. Furthermore, although the pathogenicity of WSSV identified from frozen shrimp was not evaluated, the international trade of diseased frozen shrimps could be led to the potential risk of virus transmission.

• The Korean Journal of Mycology
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• v.37 no.1
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• pp.19-27
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• 2009

This study was conducted to investigate genetic characteristics of 25 Pleurotus eringii strains that have been released in Korea based on cultural, morphological features and PCR fingerprints. Strains PER-007 and PER-012 showed distinct cultural characteristics in growth rate, morphological characteristics of mycelial colony and fruiting bodies when compared to those of other strains. Strain PER-007 did not form primordium initiation in sawdust medium and PER-012 also showed different phenotypes on fruiting bodies. Eleven URP primers were used to detect PCR polymophic bands in P. eringii strains. Primers URP1F, URP2R, URP2F, URP4R, URP6R, URP9F and URP17R were selected as useful primers for amplifying PCR polymorphic bands in P. eringii strains. The genetic similarity index was calculated by using PCR polymorphic bands amplified by eight URP primers among the 25 strains. The P. eringii strains were grouped by four distinct clusters on the UPGMA analysis. The genetic similarity values ranged from 100% to 76% were observed in three major groups, suggesting close genetic relatedness of them. Exceptionally, PER-007 and PER-017 were involved in outgroup.

• Journal of Life Science
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• v.20 no.4
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• pp.632-638
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• 2010

The genetic diversity among 48 persimmon (Diospyros kaki Thunb.) accessions, indigenous in Korea and introduced from Japan and China, was evaluated by using simple sequence repeat (SSR) markers. From 20 SSR primer sets, a total of 114 polymorphic markers were detected among 12 pollination-constant non-astringent (PCNA), 13 pollination-variant non-astringent (PVNA), 15 pollination-variant astringent (PVA), and 8 pollination-constant astringent (PCA) cultivars. Analysis of pair-wise genetic similarity coefficient (Nei-Li) and unweighted pair-group method with arithmetic averaging (UPGMA) clustering revealed two main clusters and four subclusters for cluster I. The subclustering pattern was in accordance with the classification of persimmon cultivars based on the nature of astringency loss. Phenetic relationships among the subclusters showed a closer relatedness of the PCNA group with the PVNA group, and the PVA with the PCA group. Genetic similarity co-efficiency was 0.499 on average and the highest (0.954) similarity was observed between 'Cheongdo-Bansi' and 'Haman-Bansi'. The similarity was lowest (0.192) between 'Damopan'and 'Atago'. Identification of each cultivar with the execption of 'Cheongdo-Bansi' and 'Gyeongsan-Bansi' was possible based on the SSR fingerprints, suggesting that these SSR markers are a useful tool for protecting intellectual property on newly developed cultivars.

• Journal of Plant Biotechnology
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• v.42 no.4
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• pp.401-408
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• 2015

Horticultural traits and genetic relationship were evaluated for 83 melon (Cucumis melo L.) cultivars. Survey of a total of 36 characteristics for seedling, leaf, stem, flower, fruit, and seed and subsequent multiple analysis of variance (MANOVA) were conducted. Principal component analysis (PCA) showed that 8 principle components including fruit weight, fruit length, fruit diameter, cotyledon length, seed diameter, and seed length accounted for 76.3% of the total variance. Cluster analysis of the 83 melon cultivars using average linkage method resulted in 5 clusters at coefficient of 0.7. Cluster I consisted of cultivars with high values for fruit-related traits, Cluster II for soluble solid content, and Cluster V for high ripening rate. Genotyping of the 83 cultivars was conducted using 15 expressed-sequence tagged-simple sequence repeat (EST-SSR) from the Cucurbit Genomics Initiative (ICuGI) database. Analysis of genetic relatedness by UPGMA resulted in 6 clusters. Mantel test indicated that correlation between morphological and genetic distance was very low (r = -0.11).