• Title/Summary/Keyword: Random amplified polymorphic DNA

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Isolation and Identification of a Purple, Non-Sulfur Bacterium from Korea Coast

  • Cha, Mi-Seon;Kim, Gi-Han;Son, Hyeong-Sik;Lee, Na-Eun;Lee, Jeong-Eun;Jo, Sun-Ja;Lee, Sang-Jun
    • 한국생물공학회:학술대회논문집
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    • 2003.04a
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    • pp.409-411
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    • 2003
  • A species of facultative photo-organotrophic, purple, non-sulfur bacterium was isolated from the west coast and the south coast 47 area of Korea at 2001 September. Separated 13 samples of changes with red color under $28{\sim}32\;^{\circ}C$, 3000 lux, anaerobe conditions for 7 days cultivated in Basal medium. For a pure isolation from 13 samples it used agar-shake tube method (0.4 % agar) and it separated 5 strains through 13-repetition test. The RAPD(Random Amplified Polymorphic DNA)-PCR result of strains (EGH-9, EGH-13, EGH-23, EGH-24, EGH-30) that EGH-24 and EGH-30 was same strain. For wastewater biodegradation test that 4 isolation strains cultivated in synthesis wastewater in 7 days. EGH-24 was high 63000 mg/L (CODcr) to 43400 mg/L (CODcr). EGH-24 was selected with efficient wast water treated strain. Based on the results obtained from morphology, nutrient requirements, major bacteriochlorophyll content, 165-rDNA phylogenetic analysis, this strain may be identified as a new strain of the genus Rhodobacter and named Rhodobacter sp. EGH-24.

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Identification of Fusarium Species Associated with Corn Ear Rot (옥수수 이삭썩음병에 관여하는 Fusarium속균의 동정)

  • Choi, Hyo-Won;Kim, Jung-Mi;Kim, Jin-Hee;Hong, Sung-kee;Kim, Wan-Gyu;Chun, Se-Chul
    • The Korean Journal of Mycology
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    • v.37 no.2
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    • pp.121-129
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    • 2009
  • In 2007, a total of 77 isolates of Fusarium spp. were obtained from ear rot symptoms of corns collected from 5 locations in Gangwon Province, Korea. The fungal isolates were identified based on their morphological features. Out of the isolates, fifteen isolates were identified as Fusarium verticillioides which formed microconidia in long chains on monophialides. Four isolates were identified as F. subglutinans which formed microconida only on false heads. Six isolates were identified as F. graminearum which produced red pigment in PDA culture. Besides these Fusarium species, F. napiform, F. nygamai, and F. oxysporum were identified from the rest isolates. To assess for genetic diversity of the isolates, a random amplified polymorphic DNA(RAPD) technique was carried out using URP primers. The results from the RAPD analysis showed that the isolates from corn were divided into 6 groups. These RAPD groups of the Fusarium species corresponded to morphological characters of the Fusarium species. The phylogenetic analysis of most isolates by DNA sequencing of EF-1$\alpha$ gene corresponded to morphological characters of the Fusarium species. The results of pathogenicity tests by two inoculation methods revealed that F. verticillioides, F. graminearum and F. subglutinans are strongly pathogenic to corn stalks.

Pathogenic free-living amoebae in Korea

  • Shin, Ho-Joon;Im, Kyung-Il
    • Parasites, Hosts and Diseases
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    • v.42 no.3
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    • pp.93-119
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    • 2004
  • Acanthamoeba and Naegleria are widely distributed in fresh water, soil and dust throughout the world, and cause meningoencephalitis or keratoconjunctivitis in humans and other mammals. Korean isolates, namely, Naegleria sp. YM-1 and Acanthamoeba sp. YM-2, YM-3, YM-4, YM-5, YM-6 and YM-7, were collected from sewage, water puddles, a storage reservoir, the gills of a fresh water fish, and by corneal washing. These isolates were categorized into three groups based on the mortalities of infected mice namely, highly virulent (YM-4), moderately virulent (YM-2, YM-5 and YM-7) and nonpathogenic (YM-3). In addition, a new species of Acanthamoeba was isolated from a freshwater fish in Korea and tentatively named Korean isolate YM-4. The morphologic characters of its cysts were similar to those of A. culbertsoni and A. royreba, which were previously designated as Acanthamoeba group III. Based on experimentally infected mouse mortality, Acanthamoeba YM-4 was highly virulent. The isoenzymes profile of Acanthamoeba YM-4 was similar to that of A. royreba. Moreover, an anti-Acanthamoeba YM-4 monoclonal anti-body reacted only with Acanthamoeba YM-4, and not with A. culbertsoni. Random amplified polymorphic DNA marker analysis and RFLP analysis of mitochondrial DNA and of a 188 small subunit ribosomal RNA, placed Acanthamoeba YM-4 in a separate cluster based on phylogenic distances. Thus Acanthamoeba YM-4 was identified as a new species, and assigned Acanthamoeba sohi. Up to the year 2002 in Korea, two clinical cases were found to be infected with Acanthamoeba spp. These patients died of meningoencephalitis. In addition, one case of Acanthamoeba pneumonia with an immunodeficient status was reported and Acanthamoeba was detected in several cases of chronic relapsing corneal ulcer, chronic conjunctivitis, and keratitis.

Evaluation of the Genetic Diversity of Biovar 3 Strains of Pseudomonas syringae pv. actinidiae Isolated in Korea (RAPD 지문을 통한 우리나라에서 분리된 Pseudomonas syringae pv. actinidiae biovar 3 균주의 유전적 다양성 평가)

  • Lee, Young Sun;Kim, Gyoung Hee;Koh, Young Jin;Jung, Jae Sung
    • Journal of Life Science
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    • v.30 no.1
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    • pp.1-9
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    • 2020
  • Pseudomonas syringae pv. actinidiae, the causal agent of a bacterial canker disease in kiwifruit, is subdivided into five genetically distinct populations, namely biovars 1, 2, 3, 5, and 6. Of these, strains belonging to biovar 3 are responsible for a pandemic bacterial canker of kiwifruits since 2008. This study aimed to characterize the structure of the biovar 3 population and investigate the origin of biovar 3 strains isolated in Korea. The genetic variability of fifteen biovar 3 strains, thirteen Korean and two Chinese, were evaluated through random amplified polymorphic DNA (RAPD)-PCR. The RAPD results revealed the presence of eight lineages, designated as subgroups I-VIII, across the biovar 3 strains used in this study. As the strains in subgroups II and III from China were not found in the Korean examples, we concluded that six genetically different biovar 3 subgroups (I, IV, V, VI, VII, and VIII) are present in Korea. In PCR analysis using primers specific to the strains of New Zealand and Europe, Korean strains in subgroups V and VI amplified the relevant DNA bands, suggesting that these were introduced from these two origins, respectively. PCR primers specific to subgroup VIII were developed to monitor the spread of the first biovar 3 strain in Korea, and investigations revealed that this strain was not found in Korea after its first occurrence.

Analysis of Genetic Relationship of Cordyceps militaris in Korea by Random Amplified Polymorphic DNA (한국산 번데기동충하초의 RAPD 분석에 의한 종내 그룹의 유전적 유연관계 분석)

  • Sung, Jae-Mo;Kim, Sang-Hee;Yoon, Chul-Sik;Sung, Gi-Ho;Kim, Yong-Wook
    • The Korean Journal of Mycology
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    • v.27 no.4 s.91
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    • pp.256-273
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    • 1999
  • Seventy two isolates of Cordyceps militaris collected from 11 sites in Korea, including two isolates from ATCC, were used to assess genetic variation within Cordyceps militaris. The anamorph stage and cultural characteristics of C. militaris were observed through microscope and investigated on PDA respectively. The anamorphs of C. militaris were identified to be Verticillium. Isolates of C. militaris showed different growth rates, morphology and color. Fifty six isolates of single ascospore and seventy two isolates of mass ascospore from C. militaris were analysed using by Random Amplified Polymorphic DNA (RAPD) for genetic relationship analysis. Fifty six single ascospore isolates fell into two groups by phenogram constructed from distance values using the UPGMA method in NTSYS-pc software: group A from artificial fruit body of C18 except for isolate 51; group B from artificial fruit body of C738. The average genetic distance value within group A is 0.150 and group B is 0.163. The average genetic distance value between the two groups is 0.221. The average genetic distance value within 56 single ascospores is 0.207 and 72 mass ascospores is 0.330. Genetic relationships were not found among 72 mass ascospore isolates obtained from eleven geographically distant populations.

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Characteristics and breeding of a new oyster mushroom (Pleurotus ostreatus) variety 'Chunhwashim' by using cytoplasmic hybrid (세포질전환 기법에 의한 신품종 느타리 '천화심'의 육성 및 자실체 특성)

  • Shin, Pyung-Gyun;Yoo, Young-Bok;Kong, Won-Sik;Oh, Youn-Lee
    • Journal of Mushroom
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    • v.13 no.2
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    • pp.129-134
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    • 2015
  • Hybrid strains was selected by crossing between dikaryotic strain ASI 0628 (Dagul) bred from ASI 2596 (Suhan No.3) and ASI 2782(Black pileus mutant) and monokaryotic strain ASI 2344-84. The strain 84 that shown the best cultural characteristics was selected to be a new cytoplasmic hybrid variety and named as 'Chunhwashim'. The 'Chunhwashim' shown incompatibility among them forming the confrontation growth line against parental strains ASI 0628 (Dagul) and ASI 2344 (chunchu 2ho). Fruiting body produced about $161.4{\pm}4.8g$ per bottle. And also the individual generation of fruit body is multiple than chunchu2ho as 40.9. The 'Chunhwashim' was cytoplasmic hybrid included hybrid DNA bands of parental strains ASI 0628 (Dagul) and ASI 2344 (chunchu 2ho) by Random Amplified Polymorphic DNA (RAPD) primer, and mitochondria DNA band of monokaryotic ASI 2344 (chunchu 2ho) using mitochondria microsatellite DNA marker. This new cytoplasmic hybrid variety 'Chunhwashim' of oyster mushroom is characterized by multiple of individual generation and deeply grey color of pileus.

Genetic Variation in Among Cultivated Field Populations of Korean Ginseng(Panax ginseng C.A.Meyer) Using RAPD (RAPD marker를 이용한 고려인삼(Panax ginseng C.A.Meyer)의 유전적 변이 분석)

  • 차선경;김영창;최재을;최장선;강권규
    • Korean Journal of Plant Resources
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    • v.16 no.3
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    • pp.251-256
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    • 2003
  • Genetic variation in field grown Korean ginseng(Panax ginseng C.A.Meyer) was evaluated using random amplified polymorphic(RAPD) markers. (This experiment was carried to collect the local native from farm of Chungnam National University in Korea in order to investigate genetic variation.) Some morphological characters showed considerable variation ranging 22 to 68cm in plant hight, 10 to 38mm in root diameter, 16 to 86g in root weight, and culum color and flowering date, respectively. Ten RAPD primers out of the 32 which produced reproducible bands in 662 Korean ginseng plants were selected for the further study. The total number of bands generated by 10 primers were 108 and among them 103 were polymorphic among the 662 plants with the polymorphism ratio of 94.5%. A total of 662 plants were classified into 16 groups based on polymorphic data with an URP 05 primer.

Morphological and Genetic Characteristics of Colletotrichum gloeosporioides Isolated from Newly Emerging Static-Symptom Anthracnose in Apple

  • Jeon, Yongho;Cheon, Wonsu
    • 한국균학회소식:학술대회논문집
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    • 2014.10a
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    • pp.34-34
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    • 2014
  • Filamentous fungi of the genus Colletotrichum (teleomorph, Glomerella) are considered major plant pathogens worldwide. Cereals, legumes, vegetables, and fruit trees may be seriously affected by this pathogen (1). Colletotrichum species cause typical disease symptoms known as anthracnoses, characterized by sunken necrotic tissue, where orange conidial masses are produced. Anthracnose appears in both developing and mature plant tissues (2). We investigated disease occurrence in apple orchards from 2013 to 2014 in northern Gyeongbuk province, Korea. Typical anthracnose with advanced symptoms was observed in all apple orchards studied. Of late, static fruit spot symptoms are being observed in apple orchards. A small lesion, which does not expand further and remains static until the harvesting season, is observed at the beginning of fruit growth period. In our study, static symptoms, together with the typical symptoms, were observed on apples. The isolated fungus was tested for pathogenicity on cv. 'Fuji apple' (fully ripe fruits, unripe fruits, and cross-section of fruits) by inoculating the fruits with a conidial suspension ($10^5$ conidia/ml). In apple inoculated with typical anthracnose fungus, the anthracnose symptoms progressed, and dark lesions with salmon-colored masses of conidia were observed on fruit, which were also soft and sunken. However, in apple inoculated with fungi causing static symptoms, the size of the spots did not increase. Interestingly, the shape and size of the conidia and the shape of the appressoria of both types of fungi were found to be similar. The conidia of the two types of fungi were straight and cylindrical, with an obtuse apex. The culture and morphological characteristics of the conidia were similar to those of C. gloeosporioides (5). The conidia of C. gloeosporioides germinate and form appressoria in response to chemical signals such as host surface wax and the fruitripening hormone ethylene (3). In this study, the spores started to germinate 4 h after incubation with an ethephon suspension. Then, the germ tubes began to swell, and subsequently, differentiation into appressoria with dark thick walls was completed by 8 h. In advanced symptoms, fungal spores of virtually all the appressoria formed primary hyphae within 16 h. However, in the static-symptom fungus spores, no primary hyphae formed by 16 h. The two types of isolates exhibited different growth rates on medium containing apple pectin, Na polypectate, or glucose as the sole carbon. Static-symptom fungi had a >10% reduction in growth (apple pectin, 14.9%; Na polypectate, 27.7%; glucose, 10.4%). The fungal isolates were also genetically characterized by sequencing. ITS regions of rDNA, chitin synthase 1 (CHS1), actin (ACT), and ${\beta}$-tubulin (${\beta}t$) were amplified from isolates using primer pairs ITS 1 and ITS 4 (4), CHS-79F and CHS-354R, ACT-512F and ACT-783R, and T1 and ${\beta}t2$ (5), respectively. The resulting sequences showed 100% identity with sequences of C. gloeosporioides at KC493156, and the sequence of the ${\beta}$t gene showed 100% identity with C. gloeosporioides at JX009557.1. Therefore, sequence data from the four loci studied proves that the isolated pathogen is C. gloeosporioides. We also performed random amplified polymorphic DNA-PCR, which showed clearly differentiated subgroups of C. gloeosporioides genotypes. The clustering of these groups was highly related to the symptom types of the individual strains.

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Classification of Safflower(Carthamus tinctorious L.) Collections by RAPD Analysis (RAPD 분석에 의한 홍화의 품종군 분류)

  • Bang, Kyong-Hwan;Kim, Young-Guk;Park, Hee-Woon;Seong, Nak-Sul;Cho, Joon-Hyeong;Kim, Hong-Sig;Cho, Yong-Gu
    • Korean Journal of Medicinal Crop Science
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    • v.9 no.3
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    • pp.225-231
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    • 2001
  • This studies were conducted to provide the basic information on safflower collections and to identify the variations which could be utilized in safflower breeding programs, The RAPDs was used to clarify the genetic relationships among safflower collections and to classify them into distint genetic groups. Among 30 of 10 mer primers in RAPD analysis, twenty were selected as the appropriate primers for identification of the genetic characters in safflower collections. Amplified PCR showed the highly reproducible bands at $3.0{\sim}0.2kb$. The number of bands amplified with the each primer showed the variations ranged from 2 to 11, with the average of 5.6. Total of 111 bands were identified among 20 selected primers used in PCR reaction and 84 bands (75.7%) showed polymorphism. Based on the similarity value of 0.14 in dendrogram derived from the cluster analysis using RAPD-PCR, the 30 safflower collections were classified into 11 groups. The two main groups, VII and VIII included 7 collections (23%) and 8 collections (27%), respectively. Most of the collections in group VII were the Korean collections (85%).

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Population Genetic Analyses of Gibberella fujikuroi Isolated from maize in Korea

  • Park, Sook-Young;Seo, Jeong-Ah;Lee, Yin-Won;Lee, Yong-Hwan
    • The Plant Pathology Journal
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    • v.17 no.5
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    • pp.281-289
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    • 2001
  • We analyzed 88 strains of Gibberella fujikuroi (Analmorph: Fusarium section Liseola) from maize in Korea for mating population, mating type, fumonisin production vegetative compatibility, and random amplified polymorphic DNA (RAPD) patterns. We found 50 strains that were MATA-2, 22 that were MATA-1, 1 that was MATD-1, and 15 that were not reproducibly fertile with any of the mating type testers. Of the 50 MATA-2, 15 were female fertile, while 10 of the 22 MATA-1 strains were female fertile. A total of 1,138 nitrate non-utilizing (nit) mutants were recovered from a total of 88 strains. These strains were grouped into 39 vegetative compatability groups (VCGs) by demonstrating heterokaryosis between nit mutants. A single maize ear could be infected by more than one VCG of F. moniliforme. RAPD analysis measured genetic diversity among 63 strains of F. moniliforme. Several VCGs were distinguished by RAPD fingerprinting patterns. Most strains produced significant levels of fumonisins. However, 6 MATA-2 strains from a single VCG produced higher levels of fumonisin $\textrm{B}_3$ than that of fumonisin $\textrm{B}_1$ or $\textrm{B}_2$. From these data, we concluded that most Korean strains of F. moniliforme associated with maize belonged to mating population A and produced significant levels of fumonisins. Futhermore, RAPD analysis could differentiate strains associated with different VCGs.

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