• Genomics & Informatics
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• v.16 no.3
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• pp.59-64
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• 2018

Although pork quality traits are important commercially, genome-wide association studies (GWASs) have not well considered Landrace and Yorkshire pigs worldwide. Landrace and Yorkshire pigs are important pork-providing breeds. Although quantitative trait loci of pigs are well-developed, significant genes in GWASs of pigs in Korea must be studied. Through a GWAS using the PLINK program, study of the significant genes in Korean pigs was performed. We conducted a GWAS and surveyed the gene ontology (GO) terms associated with the backfat thickness (BF) trait of these pigs. We included the breed information (Yorkshire and Landrace pigs) as a covariate. The significant genes after false discovery rate (<0.01) correction were AFG1L, SCAI, RIMS1, and SPDEF. The major GO terms for the top 5% of genes were related to neuronal genes, cell morphogenesis and actin cytoskeleton organization. The neuronal genes were previously reported as being associated with backfat thickness. However, the genes in our results were novel, and they included ZNF280D, BAIAP2, LRTM2, GABRA5, PCDH15, HERC1, DTNBP1, SLIT2, TRAPPC9, NGFR, APBB2, RBPJ, and ABL2. These novel genes might have roles in important cellular and physiological functions related to BF accumulation. The genes related to cell morphogenesis were NOX4, MKLN1, ZNF280D, BAIAP2, DNAAF1, LRTM2, PCDH15, NGFR, RBPJ, MYH9, APBB2, DTNBP1, TRIM62, and SLIT2. The genes that belonged to actin cytoskeleton organization were MKLN1, BAIAP2, PCDH15, BCAS3, MYH9, DTNBP1, ABL2, ADD2, and SLIT2.

• Research in Plant Disease
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• v.16 no.1
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• pp.10-20
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• 2010

Root-knot nematodes cause billions of dollars in crop losses annually have a broad range of host over 2,000 species of plants. These nematodes are known as obligate, sedentary endo-parasites in a plant host to feed upon to complete their life cycle. To prevent the plant parasitic nematode, methyl bromide was widely applied as a soil fumigant. Other strategies to prevent or control nematodes involve RNAi-mediated suppression, R gene transformation, natural products or chemical treatments, the expression of peptide or proteins in susceptible plants, and others. Over the last decade, the entry in GenBank for Meloidogyne reveals 73,340 ESTs and recently two complete Meloidogyne spp. genomes sequences have simultaneously been presented by two groups. Recent works have demonstrated the effect of RNAi suppression to nematode target genes. These results will provide novel members of genes as a foundation for studies focused on understanding the function of M. incognita nematode genes as well as for the development of novel target genes for parasite control. Thus the successful development of biotechnology-derived plants with nematode resistance will result in large yield benefits for producers as well as environmental benefits and will accelerate the research related to pathogensresistant crops.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.10
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• pp.1496-1511
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• 2015

The study aimed to compare the necrotic enteritis (NE)-induced transcriptome differences between the spleens of Marek's disease resistant chicken line 6.3 and susceptible line 7.2 co-infected with Eimeria maxima/Clostridium perfringens using RNA-Seq. Total RNA from the spleens of two chicken lines were used to make libraries, generating 42,736,296 and 42,617,720 usable reads, which were assembled into groups of 29,897 and 29,833 mRNA genes, respectively. The transcriptome changes were investigated using the differentially expressed genes (DEGs) package, which indicated 3,255, 2,468 and 2,234 DEGs of line 6.3, line 7.2, and comparison between two lines, respectively (fold change ${\geq}2$, p<0.01). The transcription levels of 14 genes identified were further examined using qRT-PCR. The results of qRT-PCR were consistent with the RNA-seq data. All of the DEGs were analysed using gene ontology terms, the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the DEGs in each term were found to be more highly expressed in line 6.3 than in line 7.2. RNA-seq analysis indicated 139 immune related genes, 44 CD molecular genes and 150 cytokines genes which were differentially expressed among chicken lines 6.3 and 7.2 (fold change ${\geq}2$, p<0.01). Novel mRNA analysis indicated 15,518 novel genes, for which the expression was shown to be higher in line 6.3 than in line 7.2 including some immune-related targets. These findings will help to understand host-pathogen interaction in the spleen and elucidate the mechanism of host genetic control of NE, and provide basis for future studies that can lead to the development of marker-based selection of highly disease-resistant chickens.

• BMB Reports
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• v.28 no.5
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• pp.402-407
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• 1995

Single-run Partial cDNA sequencing was conducted on 1,592 randomly selected human fetal liver cDNA clones of Korean origin to isolate novel genes related to liver functions. Each partial cDNA sequence determined was analyzed by comparing it with the databases. GenBank, Protein Information Resource (PIR) and SWISS-PROT Protein Sequence Data Bank. From a set of 1.592 cDNA clones reported here, 1,433 (90.0% of the total) were informative cDNA sequences. The other 159 clones were identified as DNA sequences which had originated from the cloning vector. Among 1,433 informative partial cDNA sequences, 851 (59.3%) clones were revealed to be identical to known human genes. These known genes have been classified into 225 different kinds of genes. In addition, 340 clones (23.7%) showed various degrees of homology to previously known human genes. Ninety four (6.6%) clones contained various repeated sequences. Twenty four (1.7%) partial cDNA sequences were found to have considerable homology to known genes from evolutionarily distant organism such as yeast, rice, Arabidopsis, mouse and rat, based on database matches, whereas 124 (8.7%) had no Significant matches. Human homologues to functionally characterized genes from different organisms could be classified as candidates for novel human genes of similar functions. Information from the partial cDNA sequences in this study may facilitate the analysis of genes expressed in human fetal liver.

• The Plant Pathology Journal
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• v.32 no.1
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• pp.8-15
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• 2016

To identify a novel biopesticide controlling rice blast disease caused by Magnaporthe oryzae, 700 plant extracts were evaluated for their inhibitory effects on mycelial growth of M. oryzae. The L. foenum-graecum Herba extract showed the lowest inhibition concentration ($IC_{50}$) of $39.28{\mu}g/ml$, which is lower than the $IC_{50}$ of blasticidin S ($63.06{\mu}g/ml$), a conventional fungicide for rice blast disease. When treatments were combined, the $IC_{50}$ of blasticidin S was dramatically reduced to $10.67{\mu}g/ml$. Since ABC transporter genes are involved in fungicide resistance of many organisms, we performed RT-PCR to investigate the transcriptional changes of 40 ABC transporter family genes of M. oryzae treated with the plant extract, blasticidin S, and tetrandrine, a recognized ABC transporter inhibitor. Four ABC transporter genes were prominently activated by blasticidin S treatment, but were suppressed by combinational treatment of blasticidin S with the plant extract, or with tetrandrine that didn't show cellular toxicity by itself in this study. Mycelial death was detected via confocal microscopy at 24 h after plant extract treatment. Finally, subsequent rice field study revealed that the plant extract had high control efficacy of 63.3% and should be considered a biopesticide for rice blast disease. These results showed that extract of L. foenum graecum Herba suppresses M. oryzae ABC transporter genes inducing mycelial death and therefore may be a potent novel biopesticide.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2022.09a
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• pp.23-23
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• 2022

Rapeseed (Brassica napus L.) is one of the most valuable oilseed crop in the world. It is widely used in various industries, such as food, animal feed, energy and chemical industries. In order to improve the industrial requirements for rapeseed, useful agronomic characteristics (higher yields and disease resistance etc.) and modified oil traits (fatty acid composition and fat content) are important in rapeseed. However, Korea has limiting genetic resources of novel traits in rapeseed. In this research, novel rapeseed mutant genotypes by mutation breeding was developed. The mutant lines were generated by the treatment of the seeds of the original cultivar 'Tamra' with 700 Gy of gamma-ray (⁶⁰Co). Mutants showing varied in flowering time, crude fat content, seed yield and fatty acid content that exhibited stable inheritance of the mutated characteristics from M₅ to M₇ generations were selected. We investigated genetic variation using SNPs identified from GBS analysis in rapeseed mutant lines derived from the gamma-ray, and interactions between the major agronomic and the oil traits. Significantly associated SNP loci were explored along with candidate genes using SNPs obtained by GBS analysis. As a results of association mapping, a total of 322 SNPs were significantly associated with agronomic traits (155 SNPs) and oil traits (167 SNPs). A total of 70 genes were annotated from agronomic characteristics SNPs; among them 7 genes significantly enriched in developmental process, and a total of 70 genes were annotated from crude fat content and fatty acid compositions SNPs; among them, 11genes were significantly enriched in biosynthetic process. These results could be used for the selection of rapeseed cultivar with enhanced qualities and potential economic benefits.

• Proceedings of the Korean Society of Sericultural Science Conference
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• 2003.04a
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• pp.72-72
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• 2003

A new Bacillus thuringiensis strain (Kl), having high toxicities to Plutella xylostella and Spodoptera exigua was isolated from Korean soil sample. It was determined to belong to subsp. kurstaki (H3a3b3c) and produced bipyramidal inclusion. PCR-RFLP analysis showed that this isolate contains three novel cryl-type crystal protein genes in addition to crylAa and crylE genes. (omitted)

• Biomedical Science Letters
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• v.25 no.3
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• pp.275-281
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• 2019

This study was performed to characterize the chromosomal metallo-${\beta}$-lactamases (MBLs) of Chryseobacterium indologenes isolated from Korea and to propose a clustering method of IND MBLs based on their amino acid similarities. Chromosomal MBL genes were amplified by PCR from 31 clinical isolates of E. indologenes. Nucleotide sequencing was performed by the dideoxy chain termination method using these PCR products. Antimicrobial susceptibilities were determined by the agar dilution method. PCR experiments showed that all 31 E. indologenes isolates contained all $bla_{IND}$ genes. DNA sequence analysis revealed that E. indologenes isolates possessed ten types of $bla_{IND}$ gene, including seven novel variants ($bla_{IND-8}$ to $bla_{IND-14}$). The most common combination of MBL was IND-2 (n = 18). Minimum inhibitory concentrations of imipenem and meropenem for the isolates harboring novel IND MBLs were ${\geq}16{\mu}g/mL$. IND MBLs were grouped in three clusters, based on amino acid similarities.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.55 no.4
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• pp.371-378
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• 2010

For sensitive and accurate gene expression analysis, normalization of gene expression data against housekeeping genes is required. There are conventional housekeeping gene (e.g. ACT) that primarily function as an internal control of transcription. In this study, we performed an in silico analysis of 278 rice gene expression samples (GSM) in order to identify the gene that is most consistently expressed. Based on this analysis, we identified novel candidate housekeeping genes that displayed improved stability among the cross experimental conditions. Furthermore four of the most conventional housekeeping genes were included in our 30 other housekeeping genes among the most stable genes. Therefore, these 30 genes can he used to normalize transcription results in gene expression studies on rice at a broad range of experimental conditions.

• Genomics & Informatics
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• v.10 no.1
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• pp.33-39
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• 2012

High-throughput genomic technologies (HGTs), including next-generation DNA sequencing (NGS), microarray, and serial analysis of gene expression (SAGE), have become effective experimental tools for cancer genomics to identify cancer-associated somatic genomic alterations and genes. The main hurdle in cancer genomics is to identify the real causative mutations or genes out of many candidates from an HGT-based cancer genomic analysis. One useful approach is to refer to known cancer genes and associated information. The list of known cancer genes can be used to determine candidates of cancer driver mutations, while cancer gene-related information, including gene expression, protein-protein interaction, and pathways, can be useful for scoring novel candidates. Some cancer gene or mutation databases exist for this purpose, but few specialized tools exist for an automated analysis of a long gene list from an HGT-based cancer genomic analysis. This report presents a new web-accessible bioinformatic tool, called CaGe, a cancer genome annotation system for the assessment of candidates of cancer genes from HGT-based cancer genomics. The tool provides users with information on cancer-related genes, mutations, pathways, and associated annotations through annotation and browsing functions. With this tool, researchers can classify their candidate genes from cancer genome studies into either previously reported or novel categories of cancer genes and gain insight into underlying carcinogenic mechanisms through a pathway analysis. We show the usefulness of CaGe by assessing its performance in annotating somatic mutations from a published small cell lung cancer study.