• Title/Summary/Keyword: GENETIC DIFFERENTIATION

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Mitochondrial DNA Polymorphism of the Japanese Anchovy (Engraulis japonicus Temminck & Schlegel) Collected from the Korean Offshore and Inshore Waters (한국근해 및 외해역에 채집된 멸치의 미토콘드리아 DNA 다양성)

  • Cho, Eun-Seob;Kim, Joo-Il
    • Journal of Life Science
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    • v.16 no.5
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    • pp.812-827
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    • 2006
  • To investigate the population structure and geographic distance among anchovies (Engraulis japonicus) in Korea, we compared and analyzed the mitochondrial DNA control region sequences (227 bp) of anchovies from 12 localities in inshore and offshore waters. The sequence analysis of 84 individuals showed 29 haplotypes, ranging in sequence divergence by pairwise comparisons from 0.3% to 3.5% (1 bp-12 bp). E9 haplotype of anchovies were found largely in inshore waters and also in offshore waters, which was regarded as the major source in Korean waters (58.3%). However, E26, E27, E28, and E29 haplotypes were found in westsouthern (locality 10, four among 7). Phylogenetic analysis using PHYLIP was divided into two clades (clade A and B). Most of the haplotypes, excluding E26, E27, E28, and E29, were strongly supported by bootstrap analysis (>75%), whereas the relationship between clade A and B was weakly supported by bootstrap analysis (51%). High levels of genetic diversity were found; haplotype diversity (H)=0.75-1.00, and nucleotide diversity $({\pi})=0.015-0.0244$. Analysis of $F_{ST}$ between populations in inshore waters ranged in 0.01-0.05, whereas those of offshore waters ranged in 0.01-0.58. A high gene flow occurred in inshore (Nm=22.61-34.22) and offshore (Nm=11.57-45.67) populations. The distribution of mitochondrial DNA haplotypes between westsouthern and other populations was suggestive of significantly different differentiation ($F_{ST}$=0.20-0.59, p<0.05; d=0.52, p=0.00; ${\phi}=0.02-0.41$, p<0.05). These results suggested that the overall anchovy population in the Korean peninsula caused considerable migration due to the mitochondrial gene flow between inshore and offshore populations to form a genetically homogenous and panmictic structure, although a heterogeneous population was found in this study.

Differentiation of Lentinus edodes Isolates in Korea by Isozyme Polymorphisms and Random Amplified Polymorphic DNA (RAPD) Analysis (Isozyme Polymorphism 및 Random Amplified Polymorphic DNA(RAPD) Pattern에 의한 표고 버섯 품종간 비교)

  • Park, Won-Mok;Ko, Han-Gyu;Park, Ro-Jo;Hong, Ki-Sung;Kim, Gyu-Hyun
    • The Korean Journal of Mycology
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    • v.25 no.3 s.82
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    • pp.176-190
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    • 1997
  • Sixty-three isolates of Lentinus edodes obtained from Korea were used to assess the genetic similarity by isozyme polymorphisms and random amplified polymorphic DNA patterns. The activities of esterase, peroxidase and acid phosphatase displayed 10, 7 and 3 distinct isozyme patterns, respectively. By combining the isozyme patterns obtained with the 3 enzymes, every isolate showed its own distinct electrophoretic phenotypes. A distance matrix calculated between all pairs of 63 electrophoretic phenotypes based on the presence or abscence of isozyme bands were analyzed by the group-average method. Results of the cluster analysis assinged the 63 phenotypes into six major groups. In the analysis of random amplified polymorphic DNA patterns, all isolates of Lentinus edodes were devided into five RAPD groups.

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Development of Sequence Characterized Amplified Regions (SCAR) Showing for Cheju Native Horse (품종 특이성을 이용한 제주마 판별 표지인자 재발)

  • Cho Byung Wook
    • Journal of Life Science
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    • v.15 no.3 s.70
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    • pp.474-478
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    • 2005
  • This study was conducted to analyze genetic characteristics and to develop the specific marker for Cheju native horse (Coo) at the level of sequence characterized amplified regions (SCARs). We collected blood samples from Cheju native horse and Thoroughbred horse (Th) and obtained genomic DNA from the blood of 50 individuals randomly selected within the breeds. Seven hundred primers were chosen randomly and were used to examin the polymorphism and 40 kinds of primers showed polymorphic RAPD band patterns between two breeds. Thirty primers of them showed horse specific bands. With the primer MG 30, amplified band of 2.0 kb showed the specificity to Cheju native horse (Cnh). Additionally MG 53 detected the thoroughbred horse (Th) specific markers at size of 2.3 kb. As the next, 2.3 kb band from MG 53 was checked with the all individuals from all the breeds of this study, and it maintained the reproducible breed specificity to thoroughbred horse (Th). With this results, 2.3 kb band was cloned into plasmid vector and sequenced bidirectionally from both ends of the cloned fragment. With the obtained sequences 10 nucleotide extended primers including the original arbitray primer were designed as a SCARs primer. Finally, the primer with extended sequence showed the reproducible breed differentiation pattern and it was possible to identify Cheju native horse (Cnh) from other breeds. The SCARs marker 2.3 kb from MG 53 could be used to identify Cheju native horse (Cnh) for not only registration but also horse breeding programe.

Multiplex Simple Sequence Repeat (SSR) Markers Discriminating Pleurotus eryngii Cultivar (큰느타리(Pleurotus eryngii) 품종 판별을 위한 초위성체 유래 다중 표지 개발)

  • Im, Chak Han;Kim, Kyung-Hee;Je, Hee Jeong;Ali, Asjad;Kim, Min-Keun;Joung, Wan-Kyu;Lee, Sang Dae;Shin, HyunYeol;Ryu, Jae-San
    • 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.

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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Transforming growth factor beta receptor II polymorphisms are associated with Kawasaki disease

  • Choi, Yu-Mi;Shim, Kye-Sik;Yoon, Kyung-Lim;Han, Mi-Young;Cha, Sung-Ho;Kim, Su-Kang;Jung, Joo-Ho
    • Clinical and Experimental Pediatrics
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    • v.55 no.1
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    • pp.18-23
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    • 2012
  • Purpose: Transforming growth factor beta receptor 2 ($TGFBR2$) is a tumor suppressor gene that plays a role in the differentiation of striated cells and remodeling of coronary arteries. Single nucleotide polymorphisms (SNPs) of this gene are associated with Marfan syndrome and sudden death in patients with coronary artery disease. Cardiovascular remodeling and T cell activation of $TGFBR2$ gene suggest that the $TGFBR2$ gene SNPs are related to the pathogenesis of Kawasaki disease (KD) and coronary artery lesion (CAL). Methods: The subjects were 105 patients with KD and 500 healthy adults as controls. Mean age of KD group was 32 months age and 26.6% of those had CAL. We selected $TGFBR2$ gene SNPs from serum and performed direct sequencing. Results: The sequences of the eleven SNPs in the $TGFBR2$ gene were compared between the KD group and controls. Three SNPs (rs1495592, rs6550004, rs795430) were associated with development of KD ($P$=0.019, $P$=0.026, $P$=0.016, respectively). One SNP (rs1495592) was associated with CAL in KD group ($P$=0.022). Conclusion: Eleven SNPs in $TGFBR2$ gene were identified at that time the genome wide association. But, with the change of the data base, only six SNPs remained associated with the $TGFBR2$ gene. One of the six SNPs (rs6550004) was associated with development of KD. One SNP associated with CAL (rs1495592) was disassociated from the $TGFBR2$ gene. The other five SNPs were not functionally identified, but these SNPs are notable because the data base is changing. Further studies involving larger group of patients with KD are needed.

Occurrence of the B- and Q-biotypes of Bemisia tabaci in Korea (담배가루이 B와 Q 계통의 국내 발생 상황)

  • Lee, Min-Ho;Kang, Seok-Young;Lee, Sun-Young;Lee, Heung-Su;Choi, June-Yeol;Lee, Gwan-Seok;Kim, Whang-Yong;Lee, Si-Woo;Kim, Seon-Gon;Uhm, Ki-Baik
    • Korean journal of applied entomology
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    • v.44 no.3 s.140
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    • pp.169-175
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    • 2005
  • The occurrence of tobacco whiteflies, Bemisia tabaci, in greenhouses was monitored in Korea in 2005. Bemisia tabaci occurred in the rose, sweet pepper, tomato, and cucumber greenhouses of Chungbuk, Chungnam, Gyongnam, and Jeonnam Provinces, but not in Jeonbuk and Gyongbuk Provinces. The biotypes and genetic differentiation of the whiteflies collected in each regions were analyzed by mitochondrial 16S DNA sequences. The 16S DNA sequences of Jincheon (Chungbuk Province) samples were similar to DNA data reported from Japan and Israel which were known as the B biotype. However, the DNA sequences of the Buyeo (Chungnam), Geoje (Gyongnam) and Boseong (Jeonnam) collections, which were 100% homologous showed over 99% similarity to the DNA of Q biotype from Spain and Egyrt. Here we report the first founding of the Q biotype in Korea. It is assumed that, unlike the B biotype reported from Jincheon since 1998, the Q biotype might have been introduced recently from the certain foreign region/country to the greenhouses in those provinces.

Molecular Characterization of Small-Spored Alternaria Species (소형의 포자를 형성하는 Alternaria 균류의 분자생물학적 특징)

  • Kim, Byung-Ryun;Park, Myung-Soo;Cho, Hye-Sun;Yu, Seung-Hun
    • Research in Plant Disease
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    • v.11 no.1
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    • pp.56-65
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    • 2005
  • To establish taxonomic system of morphologically similar species of small-spored Alternaria, phylogenetic analysis of internal transcribed spacer (ITS 1, ITS 2 and 5.8S rDNA) and mitochondrial small subunit (mt SSU) rDNA sequences and URP-PCR fingerprinting analysis from 11 species ofAlternaria were performed. Phylogenetic analysis of ITS and mt SSU rDNA sequences revealed that 10 out of 11 species of the smallspored Alternaria were phylogenetically identical with a bootstrap value of 100%. A. infectoria only was phylogenetically differentiated from the other species. The results suggest that the 10 small-spored Alternaria species are very closely related evolutionally and the markers can not be used for differentiation of the smallspored Alternaria species. URP-PCR fingerprinting analysis from eleven species of smallspored Alternaria using 10 URP primers showed that it was possible to differentiate the species, although genetic similarities were found among the species. The Alternaria sp. from common pokeweed could be distinguished from other species by URP-PCR analysis, and it was considered as a new species. A. infectoria could be easily distinguished from the other 10 species by phylogenetic analysis of ITS and mt SSU rDNA sequences and the URPPCR fingerprinting analysis.

Phytophthora Blight of Pepper and Genetic Control of the Disease (고추 역병과 그 유전적 방제)

  • Kim, Byung-Soo
    • Current Research on Agriculture and Life Sciences
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    • v.32 no.3
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    • pp.111-117
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    • 2014
  • Phytophthora blight caused by Phytophthora capsici Leonian is a dangerous disease threatening pepper growers worldwide. The efficacy of chemical control is generally low as the pathogen is soil-borne and rapidly spread by zoospores during the rainy season. Thus, based on the demand for resistant varieties, various good resistant sources, such as CM334, AC2258, and PI201234, have been reported and their inheritance of resistance studied by many different authorities. However, the mode of inheritance remains unclear, as 1 or 2 independent dominant genes, 3 genes, or multiple genes have all been reported as responsible for resistance. Recently, QTL mappings of the gene factors for resistance have been reported, and molecular markers for resistance used in breeding programs. With the release of many resistant commercial hybrid cultivars, differentiation of pathotypes of the pathogen is attracting interest among breeders and plant pathologists. Various authorities have already classified the pathogen strains into different races according to the inter-action between resistant host plants, including the source of resistance, such as CM334 and PI201234, and resistant commercial varieties and P. capsici isolates. However, no standard differential host sets have yet been established, so the results are good only for the pathogen strains used in the experiments. Thus, for breeding varieties with durable resist-ance, it is important to introduce resistance from different sources and use diverse local pathogen strains collected in the target area for distribution in a breeding program.

The Significance of Cancer Stem Cells in Canine Mammary Gland Tumors (개 유선종양 내 종양줄기세포의 중요성)

  • Park, Seo-Young;Baek, Yeong-Bin;Park, Sang-Ik;Lee, Chang-Min;Kim, Sung-Hak
    • Journal of Life Science
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    • v.31 no.2
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    • pp.248-255
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    • 2021
  • Mammary gland tumors are one of the most common cancers in female dogs, and there are various types of cells depending on the tumor type. Complex carcinoma consists of a combination of luminal epithelial and myoepithelial cells with intra-tumoral heterogeneity. However, the origins of these tumor cells and their effects on the malignancies of tumors have not been identified. Recently, it has been reported that cancer stem cells, identified in several types of human tumors, are involved in tumor heterogeneity and may also contribute to malignancies such as tumor recurrence and metastasis. Interestingly, cancer stem cells share several abilities of self-renewal and cell differentiation into multiple types of cancer cells, but they have abnormal genetic mutation and signal transduction pathways to regulate the maintenance of stem cell characters. Moreover, it is known that these cell populations contribute to cell metastasis as well as cell resistance against chemo- and radio-therapeutics that promote tumor recurrence. The existence of cancer stem cells might explain the intra-tumoral heterogeneity and cancer aggressiveness during tumorigenesis in canine mammary gland tumors. This review summarizes the characteristics and types of canine mammary gland tumors, the definition of tumor stem cells, methods of isolation, and clinical significance.