• BMB Reports
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• v.45 no.1
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• pp.47-50
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• 2012

The International HapMap Project and the Human Genome Diversity Project (HGDP) provide plentiful resources on human genome information to the public. However, this kind of information is limited because of the small sample size in both databases. A Genome-Wide Association Study has been conducted with 8,842 Korean subjects as a part of the Korea Association Resource (KARE) project. In an effort to build a publicly available browsing system for genome data resulted from large scale KARE GWAS, we developed the KARE browser. This browser provides users with a large amount of single nucleotide polymorphisms (SNPs) information comprising 1.5 million SNPs from population-based cohorts of 8,842 samples. KAREBrowser was based on the generic genome browser (GBrowse), a web-based application tool developed for users to navigate and visualize the genomic features and annotations in an interactive manner. All SNP information and related functions are available at the web site http://ksnp.cdc. go.kr/karebrowser/.

• Genomics & Informatics
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• v.6 no.2
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• pp.57-63
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• 2008

The Korean HapMap Project has been carried out for the last 5 years since it started in June, 2003. The project generated data for a sum of 1,764,000 Korean SNPs and formally registered the data to the dbSNP of NCBI (The dbSNP website. 2008). We have developed a series of software programs for association studies as well as for the comparison and analysis of Korean HapMap data with four other populations (CEPH, Yoruba, Han Chinese, and Japanese populations). The KHapmap Browser was developed and integrated to provide haplotype retrieval and comparative study tools of human ethnicities for comprehensive disease association studies (http://www.khapmap.org). On that basis, GBrowse was adopted in the KHapmap Browser for inherent Korean genetic data, and a provision of extended services was pledged with the distributed sequence annotation system (DAS). The dynamic linking service of the KHapmap Browser to other tools in our intranetwork environment provides many enhanced functions over GBrowse without DAS. KHapmap Browser is expected to be an invaluable tool for the study of Korean and international Hapmap data.

• Korean Journal of Poultry Science
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• v.44 no.2
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• pp.103-111
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• 2017

The quail (Coturnix japonica) has been used as a model animal in many research fields and its application is still expanding in other fields. Compared to the chicken, the quail is quicker to reach sexually maturity, has short generation intervals, is easy to handle, requires less space and feed, and is sturdy. In addition, it produces many eggs and the research tools developed for chicken can be applied directly to quail or with some modifications. Due to recent advances in next-generation sequencing, abundant sequence data for the quail genome and transcripts have been generated. These sequence data are valuable sources for studying functional genomics using quail, which is one of the model animal used to investigate gene function and networks. Although there are some obstacles to be removed, the quail is the best optimized model to study the functional genomics of poultry. In many research fields, functional genomics study using the quail model will provide the best opportunity to understand the phenomena and principles of life. We review why, among many other birds, the quail is the best model for studying poultry functional genomics.

• Journal of Plant Biotechnology
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• v.5 no.1
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• pp.59-61
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• 2003

Petiole explants from 20 cultivars of Catharanthus roseus were cultured on various shoot-inducing media to assess their competence for adventitious shoot formation. After eight weeks of culture on Murashige and Skoog' s medium supplemented with 4.4 $\mu\textrm{m}$6-benzyladenine and 0.5 $\mu\textrm{m}$ $\alpha$-naphthaleneacetic acid, petiole explants from 'Cooler Icy Pink' exhibited the greatest frequency of adventitious shoot formation at 40%, which was followed by 'Little Bright Eye'. By comparing with a previous study on assessment of competence for adventitious shoot formation in hypocotyl explant cultures of various cultures, it is indicated that the relative degree of their competence among cultivars varies to the organ used for the source of explant. Excised adventitious shoots were readily rooted on half-strength MS basal medium. Regenerated plantlets were successfully transplanted to potting soil and grown to maturity in a greenhouse.

• Genomics & Informatics
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• v.12 no.4
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• pp.225-230
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• 2014

Platelets are derived from the fragments that are formed from the cytoplasm of bone marrow megakaryocytes-small irregularly shaped anuclear cells. Platelets respond to vascular damage, contracts blood vessels, and attaches to the damaged region, thereby stopping bleeding, together with the action of blood coagulation factors. Platelet activation is known to affect genes associated with vascular risk factors, as well as with arteriosclerosis and myocardial infarction. Here, we performed a genome-wide association study with 352,228 single-nucleotide polymorphisms typed in 8,842 subjects of the Korea Association Resource (KARE) project and replicated the results in 7,861 subjects from an independent population. We identified genetic associations between platelet count and common variants nearby chromosome 4p16.1 ($p=1.46{\times}10^{10}$, in the KIAA0232 gene), 6p21 ($p=1.36{\times}10^{-7}$, in the BAK1 gene), and 12q24.12 ($p=1.11{\times}10^{-15}$, in the SH2B3 gene). Our results illustrate the value of large-scale discovery and a focus for several novel research avenues.

• Journal of Microbiology and Biotechnology
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• v.16 no.10
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• pp.1650-1655
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• 2006

Bacteria belonging to the genus Paenibacillus are facultatively anaerobic endospore formers and are attracting growing ecological and agricultural interest, yet their genome information is very limited. The present study surveyed the genomic features of P. polymyxa ATCC $842^T$ using pulse-field gel electrophoresis of restriction fragments and sample genome sequencing of 1,747 reads (approximately 17.5% coverage of the genome). Putative functions were assigned to more than 60% of the sequences. Functional classification of the sequences showed a similar pattern to that of B. subtilis. Sequence analysis suggests nitrogen fixation and antibiotic production by P. polymyxa ATCC $842^T$, which may explain its plant growth-promoting effects.

• Journal of Plant Biotechnology
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• v.29 no.3
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• pp.145-150
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• 2002

Biotechnology in the 21st century will be driven by three emerging technologies: genomics, high-throughput biology, and bioinformatics. These technologies are complementary to one another. A large number of economically important crops are currently subjected to whole genome sequencing. Functional genomics for determining the functions of the genes comprising the given plant genome is under progress by using various means including phenotyping data from transgenic mutants, gene expression profiling data from DNA microarrays, and metabolic profiling data from LC/mass analysis. The aim of plant molecular breeding is shifting from introducing agronomic traits such as herbicide and insect resistance to introducing quality traits such as healthful oils and proteins, which will lead to improved and nutritional food and feed products. Plant molecular breeding is also expected to aim to develop crops for producing human therapeutic and industrial proteins.

• Reproductive and Developmental Biology
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• v.35 no.4
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• pp.399-405
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• 2011

The number of abandoned dogs is increasing with the worsening of the economy and the rising of feed value. It was becoming a serious social problem because of the disease transmission and destruction of natural ecosystems by abandoned dogs been wild animal. In order to solve these problems, companion dogs necessary to secure its own genetic information and to establish the systematic tracking system. Using multiplex-PCR method with 27 microsatellite marker (MS marker) divided 3 set, various alleles occurring to 6 dog breed (Labrador Retriever, German Shepherd, English Springer Spaniel, Belgian Malinois, Jindo Dog, PoongSan Dog) make use of markers to determine allele frequency and heterozygosity. MS marker FH2834 and FH2790 have only two allele and most were found in 13 alleles at FH3381 and FH3399. Average heterozygosity of MS marker is 0.534 and especially, heterozygosity represented the highest value of 0.765 at FH3381. So, it was recognized appropriate allele frequency for individual identification and paternity diagnosis in companion dogs. Using multiplex-PCR method with MS marker, various alleles occurring to dog breed make use of markers to deter mine individual identification and paternity diagnosis, traits associated biomarkers and breed-specific marker for faster, more accurate and ways to reduce the analysis cost. Based on this result, a scientific basis was established to the existing pedigree data by applying genetics additionally. Animal registration system is expected to be conducted nationwide in future. The method expects to very useful this system.

• Genomics & Informatics
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• v.9 no.4
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• pp.152-160
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• 2011

Hypertension is the major factor of most death and high blood pressure (BP) can lead to stroke, myocardial infarction and cardiac failure. Moreover, hypertension is strongly correlated with body mass index (BMI). Although the exact causes of hypertension are still unclear, some of genetic loci were discovered from genome-wide association study (GWAS). Therefore, it is essential to study genetic variation for finding more genetic factor affecting hypertension. The purpose of our study is to conduct a CNV association study for hypertension-related traits, BP and BMI, in Korean individuals. We identified 2,206 CNV regions from 3,274 community-based Korean participants using the Affymetrix Genome-Wide Human SNP Array 6.0 platform and performed a logistic regression analysis of CNVs with two hypertension-related traits, BP and BMI. Moreover, the 4,692 participants in an independent cohort were selected for respective replication analyses. GWAS of CNV identified two loci encompassing previously known hypertension-related genes: LPA (lipoprotein) on 6q26, and JAK2 (Janus kinase 2) on 9p24, with suggestive p-values (0.0334 for LPA and 0.0305 for JAK2 ). These two positive findings, however, were not evaluated in the replication stage. Our result confirmed the conclusion of CNV study from the WTCCC suggesting weak association with common diseases. This is the first study of CNV association study with BP and BMI in Korean population and it provides a state of CNV association study with common human diseases using SNP array.

• Journal of Ginseng Research
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• v.38 no.4
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• pp.278-288
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• 2014

Background: Panax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essential. Methods: RNA-seq analysis of adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS), was performed using the Illumina HiSeq platform. After transcripts were assembled, expression profiling was performed. Results: Assemblies were generated from ~85 million and ~77 million high-quality reads from CP and CS cultivars, respectively. A total of 35,527 and 27,716 transcripts were obtained from the CP and CS assemblies, respectively. Annotation of the transcriptomes showed that approximately 90% of the transcripts had significant matches in public databases.We identified several candidate genes involved in ginsenoside biosynthesis. In addition, a large number of transcripts (17%) with different gene ontology designations were uniquely detected in adventitious roots compared to normal ginseng roots. Conclusion: This study will provide a comprehensive insight into the transcriptome of ginseng adventitious roots, and a way for successful transcriptome analysis and profiling of resource plants with less genomic information. The transcriptome profiling data generated in this study are available in our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use.