• Title/Summary/Keyword: random primer

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Genetic Diversity of Xanthomonas arboricola pv. pruni Isolated in Korea (우리나라에서 분리한 Xanthomonas arboricola pv. pruni의 유전적 다양성)

  • Park, So-Yeon;Lee, Young-Sun;Shin, Jong-Sub;Koh, Young-Jin;Jung, Jae-Sung
    • Journal of Life Science
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    • v.19 no.5
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    • pp.684-687
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    • 2009
  • Xanthomonas arboricola pv. pruni, the causal agent of bacterial shot holes in stone fruits, was known to have a low population diversity. To investigate the genetic characteristics of X. arboricola pv. pruni isolated in Korea, three strains which have identical 16S rDNA sequences - including type strain (LMG852), Japanese isolate (MAFF301420) and Korean isolate (XWD1) - were analysed based on the nucleotide sequences of three DNA regions and RAPD pattern. No sequence diversity among the three strains was found within the ITS, glnA and atpD gene sequences. However, five of 756 nucleotides of the atpD gene determined (accession number FJ429319) were different from those of the French strain available from the Genbank database. RAPD analyses performed with 40 different arbitrary primers revealed that two strains isolated from Korea and Japan showed similarity in their band patterns distinguished by type strain. These results suggest that Korean and Japanese strains are very close and belong to a population with a low genetic diversity, and might have a different origin from strains found in West Europe.

Genetic Relationship among Sedum Species Based on Morphological Characteristics and RAPD Analysis (한국산 Sedum속 식물의 형태적 특성과 RAPD에 의한 유연관계 분석)

  • Kwon, Soon Tae;Jeong, Jeong Hag
    • Horticultural Science & Technology
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    • v.17 no.4
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    • pp.489-493
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    • 1999
  • This study was conducted to investigate the potentiality of various Korean Sedum species as ornamental plants based on morphological characteristics and to analyze the genetic relationship among the Sedum species. S. kamtschaticum and S. takesimense possessing splendour flowercluster with yellow color could be suggested for garden plant, S. routundifolium having pink flower-clusters with round leaf shape for pot flower or garden plant and S. sarmentosum, S. polystichoides and S. oryzifolium with creeping stem and low plant height for ground cover plant or floral carpet. Eighteen oligonucleotide random primers were used to amplify genomic DNA of Sedum species using polymerase chain reaction (PCR). Ninety five polymorphic bands among 125 different DNA fragments in the range of 224 to 3,675 base pairs were obtained from RAPD analysis. Similarity matrix of RAPD profiles was generated by coefficient value of variation, and the data were subjected to be cluster analysis. Fifteen lines of Sedum species analyzed were classified into 3 groups with the similarity coefficient value of 0.418, and 12 groups with the value of 0.328. RAPD results showed similar trends as the morphological characteristics of the plants.

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Characterization of a New Cultivar "Dan Bi" by Mono-mono Hybridization in Pleurotus eryngii (단핵균주간 교잡에 의한 큰느타리버섯 신품종 "단비"의 특성)

  • Kim, Min-Keun;Ryu, Jae-San;Yoo, Young-Bok
    • The Korean Journal of Mycology
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    • v.39 no.1
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    • pp.39-43
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    • 2011
  • A new cultivar "Dan Bi" of Pleurotus eryngii was developed by the method of mono-mono crossing between monokaryotic strains derived from KNR2312 and KNR2596. The parental strains, KNR2312 and KNR2596, are characterized by the property of high quality and a small number of primordia formation, respectively. The optimum temperature of mycelial growth was 25 and that of fruiting body development was $15{\sim}16^{\circ}C$. The period of harvesting including primordia formation was 0.7~1.3 days later than that of control strain Knneutari No. 3 in the culling cultivation. The color of pileus and stipe surface was neutral-brown and pure white, respectively. The shape of pileus was dome and has a scale like as cobweb. The yield was $93{\pm}9.7$ g per 850 cc of plastic bottle. Analysis of the genetic characteristics of the new commercial variety "Dan Bi" showed a different profile as that of the control strain, Knneutari No. 3, when RAPD (Random Amplified Polymorphic DNA) primer #8005 was used. This new variety "Dan Bi" of Pleurotus eryngii is characterized by a small number of primordia formation after scratching.

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 Relationship of Genus Rosa Germplasm and Genetic Diversity of Rosa rugosa in Korea (장미속 유전자원의 유전적 관계와 국내 해당화의 유전적 다양성)

  • Joung, Youn-Hwa;Kim, Seung-Tae;Kim, Gi-Jun;Lee, Ja-Hyun;Gi, Gwang-Yeon;Han, Tae-Ho
    • Horticultural Science & Technology
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    • v.28 no.6
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    • pp.1003-1013
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    • 2010
  • Fifty-nine accessions of 23 species in genus Rosa were collected, and 15 accessions of Rosa rugosa were collected throughout 10 regions of Korea. Their genetic relationship was investigated by using morphological analysis and RAPD marker. The morphological analysis was measured for 7 quantitative and quantified for 4 qualitative traits. RAPD analysis obtained a total of 959 polymorphic bands by using twenty primers. Morphological analysis classified most according to the rose section system except for several species. The cluster analysis of genus Rosa based on RAPD data could identify the subgenus $Platyrhodon$ and $Eurosa$. The subgenus $Eurosa$ separated five sections; $Gallicanae$, $Cinnamomeae$, $Pimpinellifoliae$, $Synstylae$ and $Caninae$. Correlation analysis between morphological and RAPD analysis showed low significance ($r$ = 0.35). The accessions of R. rugosa belonged to the section $Cinnamomeae$ clustered into three groups at genetic distance ranging from 0.28 on the base of RAPD analysis. In conclusion, the genetic relationship of the genus Rosa was consistent to the previously reported rose section system, and domestic collections of $R.$ $rugosa$ were separated from 3 groups on the base of RAPD marker.

Genetic Relationships among the Parental Bombyx mori Strains of the Current F$_1$ Hybrid Silkworm based on RAPD (RAPD를 이용한 장려누에품종의 원종간 유전적 유연관계)

  • 황재삼;이진성;강현아;이상몽;손해룡
    • Korean journal of applied entomology
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    • v.36 no.3
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    • pp.206-214
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    • 1997
  • The genetic relationships among the twenty parental silkworm, Bombyx mori strains authorized in Korea were evaluated using RAPDs-PCR(Random Amplified Polymorphic DNAs-Polymerase Chain Reaction). Twenty-six different 10-mer oligonucleotide primers were used to screen genetic characteristics of parental twenty silkworm strains by RAPD-PCR analysis. 24 primers showed different banding patterns among the strains. Based on these RAPD patterns, the genetic relationships among the silkworm strains were analyzed by UPGMA(Unweighed Pair-Group Method with Arithmetic average) method. The phylogenetic relationships in the twenty silkworm strains were classified into two major sub-groups at the genetic similarity coefficient of 0.60. The first sub-group included Jaml13, Jaml 19, Jaml20, Jam123, Jam1 25 and Jam 127. Jamll4, Jam1 2 I, Jam 122, Jam 124, Jam1 26, Jam 128, Jam129, Jam 130, Jam 131, Jam1 32, Jam133, Jam134, Jam301 and Jam302 were included in the 2nd group. The genetic distance values among Jam1 14, Jam120 and Jam127 were lower than those among the other strains, while Jam129 is very closely related to Jam131 as showing coefficient value of 1 .O.

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Genetic Polymorphism of Microsatellite Markers in Panax ginseng C.A. Meyer (인삼 (Panax ginseng C.A. Meyer)의 Microsatellite 마커에 대한 유전적 다형성과 특성 규명)

  • Park, Sun-Wha;Hyun, Young-Se;Chung, Ki-Wha
    • Journal of Ginseng Research
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    • v.33 no.3
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    • pp.199-205
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    • 2009
  • Ginseng (Panax ginseng C.A. Meyer) is one of the most important medicinal plants in East Asia. Microsatellite or simple sequence repeat (SSR) markers are used in obtaining genetic analysis and authentication in many plants. The present study examined five microsatellites in conjunction with P. ginseng in Korea. The total observed allelic number was 17 (mean = 3.4), and gene diversities varied from 0.078 to 0.543 with an average of 0.314. Through a combined analysis of five loci in 100 ginseng samples, 44 different combined genotypes were observed. Expected and observed heterozygosites ranged from 0.077 to 0.541 (mean = 0.313) and 0.040 to 0.130 (0.083), respectively. All examined loci exhibited deficiency of heterozygosity and deviation from the Hardy-Weinberg equilibrium. Such results may be explained by the non-random mating and inbreeding that has occurred for several hundred years. These microsatellite markers could be used for the study of molecular genetics and the establishment of DNA marker database, as well as authentication of ginseng species and chromosomal mapping of QTL loci in P. ginseng.

The Screening and Characterization of Promoters Inducible by Superoxide Radical in Escherichia coli (대장균에서 Superoxide 라디칼에 의하여 유도되는 프로모터의 탐색 및 특성 분석)

  • 고영상;노정혜
    • Korean Journal of Microbiology
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    • v.31 no.4
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    • pp.267-273
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    • 1993
  • We screened promoters inducible by superoxide radical from Escherichia coli. For this. we constructed random promoter library from E. coli MG 1655 using a promoter-probing plasmid. pJAC4. Six hundred and sixty clones in this library were classified based on their promoter strength by ampicillin gradient plate assay. Three hundred and eighty three clones with relatively weak to medium promoter strength were selected and then screened for their inducibility by superoxide radical on ampicillin gradient plate containing paraquat. Three clones (clones 5. 15 and 34) were detected to be induced by paraquat treatment and the level of induction were between 1.4 and 4 folds. Comparison of nucleotide sequences of the cloned promoter fragment with registered sequences in GENBANK and EMBL databases suggests that the cloned DNA fragments have not been yet characterized in E. coli. Transcription start sites in these clones were determined by rrimer extension and S I nuclease protection analysis. S 1 analysis of clones 5 and IS indicated that the mRNA levels were increased by paraquat treatment. Especially. clone 5 \vas found to have two transcription start sites. the upstream start site of which was selectively used by paraquat treatment. Searching for promoter clements. we found that only the downstream promoter of clone 5 has -10 and - 35 promoter elements recognized by RNA polymerase ($E\sigma^{70}$) and the others have no conserved promoter elements. This suggests that these superoxideinducible promoters may require transcription initiation protein(s) other than $E\sigma^{70}$.

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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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Comparative Genetic Characteristics of Korean Ginseng using DNA Markers (분자지표를 이용한 고려인삼의 유전적 특성 비교)

  • Shin, Mi Ran;Jo, Ick Hyun;Chung, Jong Wook;Kim, Young Chang;Lee, Seung Ho;Kim, Jang Uk;Hyun, Dong Yun;Kim, Dong Hwi;Kim, Kee Hong;Moon, Ji Young;Noh, Bong Soo;Kang, Sung Taek;Lee, Dong Jin;Bang, Kyong Hwan
    • Korean Journal of Medicinal Crop Science
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    • v.21 no.6
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    • pp.444-454
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    • 2013
  • The development of random amplified polymorphic DNA (RAPD) and expressed sequence tag-derived simple sequence repeats (EST-SSRs) provided a useful tool for investigating Korean ginseng genetic diversity. In this study, 18 polymorphic markers (7 RAPD and 11 EST-SSR) selected to assess the genetic diversity in 31 ginseng accessions (11 Korean ginseng cultivars and 20 breeding lines). In RAPD analysis, a total of 53 unique polymorphic bands were obtained from ginseng accessions and number of amplicons ranged from 4 to 11 with a mean of 7.5 bands. Pair-wise genetic similarity coefficient (Nei) among all pairs of ginseng accessions varied from 0.01 to 0.32, with a mean of 0.11. On the basis of the resulting data, the 31 ginseng accessions were grouped into six clusters. As a result of EST-SSR analysis, 11 EST-SSR markers detected polymorphisms among the 31 ginseng accessions and revealed 49 alleles with a mean of 4.45 alleles per primer. The polymorphism information content (PIC) value ranged from 0.06 to 0.31, with an average of 0.198. The 31 ginseng accessions were classified into five groups by cluster analysis based on Nei's genetic distances. Consequently, the results of ginseng-specific RAPD and EST-SSR markers may prove useful for the evaluation of genetic diversity and discrimination of Korean ginseng cultivars and breeding lines.