• Mycobiology
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• v.45 no.4
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• pp.401-408
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• 2017

Colletotrichum gloeosporioides is an economically important fungal pathogen causing substantial yield losses indifferent host plants. To understand the genetic diversity and molecular epidemiology of this fungus, we have developed a novel, high-resolution multi-locus microsatellite typing (MLMT) method. Bioinformatic analysis of C. gloeosporioides unannotated genome sequence yielded eight potential microsatellite loci, of which five, CG1 $(GT)_n$, CG2 $(GT1)_n$, CG3 $(TC)_n$, CG4 $(CT)_n$, and CG5 $(CT1)_n$ were selected for further study based on their universal amplification potential, reproducibility, and repeat number polymorphism. The selected microsatellites were used to analyze 31 strains of C. gloeosporioides isolated from 20 different host plants from India. All microsatellite loci were found to be polymorphic, and the approximate fragment sizes of microsatellite loci CG1, CG2, CG3, CG4, and CG5 were in ranges of 213-241, 197-227, 231-265, 209-275, and 132-188, respectively. Among the 31 isolates, 55 different genotypes were identified. The Simpson's index of diversity (D) values for the individual locus ranged from 0.79 to 0.92, with the D value of all combined five microsatellite loci being 0.99. Microsatellite data analysis revealed that isolates from Ocimum sanctum, Capsicum annuum (chili pepper), and Mangifera indica (mango) formed distinct clusters, therefore exhibited some level of correlation between certain genotypes and host. The developed MLMT method would be a powerful tool for studying the genetic diversity and any possible genotype-host correlation in C. gloeosporioides.

• The Plant Pathology Journal
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• v.36 no.6
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• pp.591-599
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• 2020

Phytophthora root and stem rot reduce soybean yields worldwide. The use of R-gene type resistance is currently crucial for protecting soybean production. The present study aimed to identify the genomic location of a gene conferring resistance to Phytophthora sojae isolate 2457 in the recombinant inbred line population developed by a cross of Daepung × Daewon. Singlemarker analysis identified 20 single nucleotide polymorphisms associated with resistance to the P. sojae isolate 2457, which explained ~67% of phenotypic variance. Daewon contributed a resistance allele for the locus. This region is a well-known location for Rps1 and Rps7. The present study is the first, however, to identify an Rps gene locus from a major soybean variety cultivated in South Korea. Linkage analysis also identified a 573 kb region on chromosome 3 with high significance (logarithm of odds = 13.7). This genomic region was not further narrowed down due to lack of recombinants within the interval. Based on the latest soybean genome, ten leucine-rich repeat coding genes and four serine/ threonine protein kinase-coding genes are annotated in this region, which all are well-known types of genes for conferring disease resistance in crops. These genes would be candidates for molecular characterization of the resistance in further studies. The identified R-gene locus would be useful in developing P. sojae resistant varieties in the future. The results of the present study provide foundational knowledge for researchers who are interested in soybean-P. sojae interaction.

• Korean Journal of Microbiology
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• v.54 no.3
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• pp.175-187
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• 2018

Myxobacteria produce diverse secondary metabolites for predation, self-defense, intercellular signaling, and other unknown functions. Many secondary metabolites isolated from myxobacteria show pharmaceutically useful bioactivity such as anticancer, antibacterial, and antifungal activities with a unique mechanism of action. Therefore, a large number of myxobacterial strains have been isolated globally and many bioactive compounds have been purified from them. However, 16S rRNA database analysis indicates that there are far more types of myxobacterial species in the wild than have ever been isolated, and genome sequence analysis suggests that each myxobacterium is capable of producing much more metabolites than already known. In this article, the current status of studies on the secondary metabolites from myxobacteria, their biosynthetic genes, biological functions, and transcriptional regulatory factors governing gene expression were reviewed.

• Korean Journal of Plant Tissue Culture
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• v.28 no.2
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• pp.75-79
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• 2001

An experiment was carried out to introduce OsHSP17.9, a low molecular HSP gene isolated from rice plant to orchardgrass (Dactylis glomerata L.) using Agrobacterium. Mature seed-derived calli of orchardgrass were co-cultured with Agrobacterium tumefaciens EHA101 harboring the plasmid pIG-HSP17.9 for transformation. Calli selected by hygromycin were transferred to N$_{6}$ medium containing 1 mg/L NAA, 5 mg/L kinetin, 250 mg/L cefotaxime and 50 mg/L hygromycin and several hygromycin resistant plants were obtained. Stable incorporation of the introduced OsHSP17.9 to the genome of the hygromycin resistant plants was confirmed by PCR and Southern blot analysis. Transformation efficiency was variable between cultivars in which it was 16.5% in Potomac and 8.0% in Frontier. Constitutive expression of the transgene in the transformed orchardgrass tissues was identified by Northern blot analysis but transcript levels were different among individual plants.s.

• Journal of Plant Biotechnology
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• v.38 no.3
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• pp.209-214
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• 2011

Transgenic lettuce plants were successfully obtained from hypocotyl explants inoculated with Agrobacterium tumefaciens, which harbored a binary vector plasmid with Bcl-2 gene, related to apoptosis. After culture and selection on MS medium a number of kanamycin-resistant plantlets were regenerated. Polymerase chain reaction, Southern blot analysis and Northern blot analysis were used to identify and characterize the transgenic plants with the integrated Bcl-2 gene. Over 100 transgenic plants have been established in soil and flowered in the greenhouse. T1 progeny of 100 transgenic lettuce inbred lines were inoculated with Sclerotinia sclerotiorum. Expression of the Bcl-2 peptide in transgenic lettuce plants provides high levels of field resistance against Sclerotinia sclerotiorum, causal agent of the agronomically important fungal disease of lettuce.

• Mycobiology
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• v.49 no.5
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• pp.491-497
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• 2021

An endolichenic fungus Xylaria grammica EL000614 produces grammicin, a potent nematicidal pyrone derivative that can serve as a new control option for root-knot nematodes. We optimized an Agrobacterium tumefaciens-mediated transformation (ATMT) protocol for X. grammica to support genetic studies. Transformants were successfully generated after co-cultivation of homogenized young mycelia of X. grammica with A. tumefaciens strain AGL-1 carrying a binary vector that contains the bacterial hygromycin B phosphotransferase (hph) gene and the eGFP gene in T-DNA. The resulting transformants were mitotically stable, and PCR analysis showed the integratin of both genes in the genome of transformants. Expression of eGFP was confirmed via fluorescence microscopy. Southern analysis showed that 131 (78.9%) out of 166 transformants contained a single T-DNA insertion. Crucial factors for producing predominantly single T-DNA transformants include 48 h of co-cultivation, pretreatment of A. tumefaciens cells with acetosyringone before co-cultivation, and using freshly prepared mycelia. The established ATMT protocol offers an efficient tool for random insertional mutagenesis and gene transfer in studying the biology and ecology of X. grammica.

• Genomics & Informatics
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• v.19 no.2
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• pp.17.1-17.13
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• 2021

Breast cancer is one of the leading causes of cancer in women all over the world and accounts for ~25% of newly observed cancers in women. Epigenetic modifications influence differential expression of genes through non-coding RNA and play a crucial role in cancer regulation. In the present study, epigenetic regulation of gene expression by in-silico analysis of histone modifications using chromatin immunoprecipitation sequencing (ChIP-Seq) has been carried out. Histone modification data of H3K4me3 from one normal-like and four breast cancer cell lines were used to predict miRNA expression at the promoter level. Predicted miRNA promoters (based on ChIP-Seq) were used as a probe to identify gene targets. Five triple-negative breast cancer (TNBC)-specific miRNAs (miR153-1, miR4767, miR4487, miR6720, and miR-LET7I) were identified and corresponding 13 gene targets were predicted. Eight miRNA promoter peaks were predicted to be differentially expressed in at least three breast cancer cell lines (miR4512, miR6791, miR330, miR3180-3, miR6080, miR5787, miR6733, and miR3613). A total of 44 gene targets were identified based on the 3'-untranslated regions of downregulated mRNA genes that contain putative binding targets to these eight miRNAs. These include 17 and 15 genes in luminal-A type and TNBC respectively, that have been reported to be associated with breast cancer regulation. Of the remaining 12 genes, seven (A4GALT, C2ORF74, HRCT1, ZC4H2, ZNF512, ZNF655, and ZNF608) show similar relative expression profiles in large patient samples and other breast cancer cell lines thereby giving insight into predicted role of H3K4me3 mediated gene regulation via the miRNA-mRNA axis.

• Nutrition Research and Practice
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• v.13 no.4
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• pp.316-322
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• 2019

BACKGROUND/OBJECTIVES: The association between dietary patterns and depression has been reported but the results have been inconsistent. This study was conducted to investigate the association between dietary patterns and depression in middle-aged Korean adults. SUBJECTS/METHODS: The participants were selected from a community-based cohort, a subset of the Korean Genome and Epidemiology Study. Depression was assessed using the Korean version of the Beck Depression Inventory (BDI) and those with a BDI score ${\geq}16$ were defined as having depression. The subjects' food intakes over the year preceding the survey were estimated by using a validated semi-quantitative food frequency questionnaire. Dietary patterns were identified by using factor analysis. Multiple logistic regression was used to assess the association of dietary pattern with depression. RESULTS: Among 3,388 participants, 448 (13.2%) were identified as having depression. We identified two major dietary patterns: 'Healthy' dietary pattern was characterized by high intakes of vegetables, soybeans, mushroom, seaweeds, white fish, shellfish and fruits and a low intake of white rice. 'Unhealthy' dietary pattern was characterized by high intakes of white rice, meats, ramen, noodles, bread and coffee and a low intake of rice with other grains. Compared with subjects in the lowest quartiles, those in the highest quartiles of the healthy dietary pattern had a significantly lower odds ratio (OR = 0.59, 95% CI: 0.42-0.82, P for trend = 0.0037) after adjusting for potential confounders. In contrast, the unhealthy dietary pattern was negatively associated with depression (OR = 1.65, 95% CI: 1.19-2.28, P for trend = 0.0021). CONCLUSION: This results suggest that a healthy dietary pattern (rich in vegetables, soybeans, mushroom, seaweeds, white fish, shellfish, and fruits) is associated with low risk of depression. Whereas an unhealthy dietary pattern (rich in white rice, meats, ramen, noodles, bread, and coffee) is associated with a high risk of depression in middle-aged Korean adults.

• The Plant Pathology Journal
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• v.35 no.1
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• pp.41-50
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• 2019

Sugarcane bacilliform viruses (SCBV), which belong to the genus Badnavirus, family Caulimoviridae, are an important DNA virus complex that infects sugarcane. To explore the genetic diversity of the sugarcane-infecting badnavirus complex in China, we tested 392 sugarcane leaf samples collected from Fujian, Yunnan, and Hainan provinces for the occurrence of SCBV by polymerase chain reaction (PCR) assays using published primers SCBV-F and SCBV-R that target the reverse transcriptase/ribonuclease H (RT/RNase H) regions of the viral genome. A total of 111 PCR-amplified fragments (726 bp) from 63 SCBV-positive samples were cloned and sequenced. A neighbor-joining phylogenetic tree was constructed based on the SCBV sequences from this study and 34 published sequences representing 18 different phylogroups or genotypes (SCBV-A to -R). All SCBV-tested isolates could be classified into 20 SCBV phylogenetic groups from SCBV-A to -T. Of nine SCBV phylogroups reported in this study, two novel phylogroups, SCBV-S and SCBV-T, that share 90.0-93.2% sequence identity and show 0.07-0.11 genetic distance with each other in the RT/RNase H region, are proposed. SCBV-S had 57.6-92.2% sequence identity and 0.09-0.66 genetic distance, while SCBV-T had 58.4-90.0% sequence identity and 0.11-0.63 genetic distance compared with the published SCBV phylogroups. Additionally, two other Badnavirus species, Sugarcane bacilliform MO virus (SCBMOV) and Sugarcane bacilliform IM virus (SCBIMV), which originally clustered in phylogenetic groups SCBV-E and SCBV-F, respectively, are first reported in China. Our findings will help to understand the level of genetic heterogeneity present in the complex of Badnavirus species that infect sugarcane.

• Journal of Ginseng Research
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• v.43 no.4
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• pp.572-579
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• 2019

Background: Panax ginseng has been used in traditional medicine to strengthen the body and mental well-being of humans for thousands of years. Many elite ginseng cultivars have been developed, and ginseng cultivation has become well established during the last century. However, heat stress poses an important threat to the growth and sustainable production of ginseng. Efforts have been made to study the effects of high temperature on ginseng physiology, but knowledge of the molecular responses to heat stress is still limited. Methods: We sequenced the transcriptomes (RNA-Seq) of two ginseng cultivars, Chunpoong (CP) and Yunpoong (YP), which are sensitive and resistant to heat stress, respectively, after 1- and 3-week heat treatments. Differential gene expression and gene ontology enrichment along with profiled chlorophyll contents were performed. Results: CP is more sensitive to heat stress than YP and exhibited a lower chlorophyll content than YP. Moreover, heat stress reduced the chlorophyll content more rapidly in CP than in YP. A total of 329 heat-responsive genes were identified. Intriguingly, genes encoding chlorophyll a/b-binding proteins, WRKY transcription factors, and fatty acid desaturase were predominantly responsive during heat stress and appeared to regulate photosynthesis. In addition, a genome-wide scan of photosynthetic and sugar metabolic genes revealed reduced transcription levels for ribulose 1,5-bisphosphate carboxylase/oxygenase under heat stress, especially in CP, possibly attributable to elevated levels of soluble sugars. Conclusion: Our comprehensive genomic analysis reveals candidate loci/gene targets for breeding and functional studies related to developing high temperature-tolerant ginseng varieties.