• Journal of Crop Science and Biotechnology
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• v.10 no.3
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• pp.147-158
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• 2007

Xanthomonas axonopodis pv. glycines(Xag) is a pathogen that causes bacterial leaf pustule(BLP) disease in soybeans grown in Korea and the southern United States. Typical and early symptoms of the disease are small, yellow to brown lesions with raised pustules that develop into large necrotic lesions leading to a substantial loss in yield due to premature defoliation. After Xag infects PI 96188, only pustules without chlorotic haloes were observed, indicating the different response to Xag. To identify differentially expressed genes prior to and 24 hr after Xag inoculation to PI 96188 and BLP-resistant SS2-2, an oligonucleotide macroarray was constructed with 100 genes related to disease resistance and metabolism from soybean and Arabidopsis. After cDNAs from each genotype were applied on the oligonucleotide macroarrays with three replicates and dye swapping, 36 and 81 genes were expressed as significantly different between 0 hr and 24 hr in PI 96188 and SS2-2, respectively. Six UniGenes, such as the leucine-rich repeat protein precursor or 14-3-3-like protein, were selected because they down-regulated in PI 96188 and up-regulated in SS2-2 after Xag infection, simultaneously. Using tubulin and cDNA of Jangyeobkong(BLP-susceptible) as controls, the oligonucleotide macroarray data concurred with quantitative real-time RT-PCR(QRT RT-PCR) results in most cases, supporting the accuracy of the oligonucleotide macroarray experiments. Also, QRT RT-PCR data suggested six candidate genes that might be involved in a necrotic response to Xag in PI 96188.

• Mycobiology
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• v.37 no.3
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• pp.230-237
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• 2009

The oyster mushroom (Pleurotus ostreatus) is one of the most important edible mushrooms worldwide. The mechanism of P. ostreatus fruiting body development has been of interest both for the basic understanding of the phenotypic change of the mycelium-fruiting body and to improve breeding of the mushrooms. Based on our previous publication of P. ostreatus expressed sequence tag database, 1,528 unigene clones were used in macroarray analysis of mycelium, fruiting body and basidiospore developmental stages of P. ostreatus. Gene expression profile databases generated by evaluating expression levels showed that 33, 10, and 94 genes were abundantly expressed in mycelium, fruiting body and basidiospore developmental stages, respectively. Among them, the genes specifically expressed in the fruiting body stage were further analyzed by reverse transcription-polymerase chain reaction and Northern blot to investigate temporal and spatial expression patterns. These results provide useful information for future studies of edible mushroom development.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2001.10a
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• pp.117-150
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• 2001

cDNA Microarray 처리를 위한 시스템 개발에 관하여 개발시의 주요 착안점과 이전의 시스템에 비해서 개선된 몇 가지 기술에 대하여 본 연구팀의 실제적인 개발경험을 중심으로 설명한다. 렬 연구팀에서 만든 시스템의 기능은 이미지 처리부터 군집화(Clustering)에 이르는 전 과정을 통합적으로 처리될 수 있는데, 이 각 과정에 대하여 개략적으로 설명한다. 그리고 이 시스템을 활용하여 Macroarray라고 불릴 수 있는 새로운 형식의 array 실험장치에 어떻게 본 시스템이 적용되는지에 대하여도 설명을 한다.

• The Plant Pathology Journal
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• v.35 no.3
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• pp.257-273
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• 2019

Tomato (Solanum lycopersicum) is one of the most widely grown and economically important vegetable crops in the world. Tomato chlorosis virus (ToCV) is one of the recently emerged viruses of tomato distributed worldwide. ToCV-tomato interaction was investigated at the molecular level for determining changes in the expression of tomato genes in response to ToCV infection in this study. A cDNA library enriched with genes induced in response to ToCV infection were constructed and 240 cDNAs were sequenced from this library. The macroarray analysis of 108 cDNAs revealed that the expression of 92 non-redundant tomato genes was induced by 1.5-fold or greater in response to ToCV infection. The majority of ToCV-induced genes identified in this study were associated with a variety of cellular functions including transcription, defense and defense signaling, metabolism, energy, transport facilitation, protein synthesis and fate and cellular biogenesis. Twenty ToCV-induced genes from different functional groups were selected and induction of 19 of these genes in response to ToCV infection was validated by RT-qPCR assay. Finally, the expression of 6 selected genes was analyzed in different stages of ToCV infection from 0 to 45 dpi. While the expression of three of these genes was only induced by ToCV infection, others were induced both by ToCV infection and wounding. The result showed that ToCV induced the basic defense response and activated the defense signaling in tomato plants at different stages of the infection. Functions of these defense related genes and their potential roles in disease development and resistance to ToCV are also discussed.

• The Plant Pathology Journal
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• v.33 no.1
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• pp.80-86
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• 2017

One of the major problems in strawberry production is difficulty in diagnosis of anthracnose caused by Colletotrichum acutatum or Glomerella cingulata in latent infection stage. We here developed a diagnostic tool for the latent infection consisting of initial culturing of fungi, DNA extraction, synthesis of PCR-amplified probes and microtube hybridization (MTH) using a macroarray. The initial culturing step is convenient to lure the fungi out of the plant tissues, and to extract PCR-inhibitor-free DNA directly from fungal hyphae. For specific detection of the fungi, PCR primers were designed to amplify the fungal MAT1-2 gene. The subsequent MTH step using the PCR products as probes can replace the laborious electrophoresis step providing us sequence information and high-throughput screening. Using this method, we have conducted a survey for a few thousands nursery plants every year for three consecutive years, and finally succeeded in eliminating latent infection in the third year of challenge.

• The Plant Pathology Journal
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• v.30 no.2
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• pp.208-214
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• 2014

Wild rice, Oryza grandiglumis shows hyper-resistance response to pathogen infection. In order to identify genes necessary for defense response in plants, we have carried out a subtractive hybridization coupled with a cDNA macroarray. An acidic PATHOGENESIS-RELATED1 (PR1) gene of the wild rice is highly identical to the acidic PR1 genes of different plant species. The OgPR1a cDNA has an apparent single open reading frame with a predicted molecular mass 40,621 Da and an isoelectic point of 5.14. Both in silico analysis and a transient expression assay in onion epidermal cells revealed that the OgPR1a protein could be localized in intercellular space in plants. The OgPR1a mRNA was strongly transcribed by the exogenous treatment with ethylene and jasmonic acid as well as protein phosphatase inhibitors. Additionally, ectopic expression of the OgPR1a conferred disease resistance on Arabidopsis to the bacterial and fungal infections.