• Genomics & Informatics
• /
• v.4 no.2
• /
• pp.80-86
• /
• 2006

It is clear that the construction of large insert DNA libraries is important for map-based gene cloning, the assembly of physical maps, and simple screening for specific genomic sequences. The bacterial artificial chromosome (BAC) system is likely to be an important tool for map-based cloning of genes since BAC libraries can be constructed simply and analyzed more efficiently than yeast artificial chromosome (YAC) libraries. BACs have significantly expanded the size of fragments from eukaryotic genomes that can be cloned in Escherichia coli as plasmid molecules. To facilitate the isolation of molecular-biologically important genes in Ashbya gossypii, we constructed Ashbya chromosome-specific BAC libraries using pBeloBAC11 and pBACwich vectors with an average insert size of 100 kb, which is equivalent to 19.8X genomic coverage. pBACwich was developed to streamline map-based cloning by providing a tool to integrate large DNA fragments into specific sites in chromosomes. These chromosome-specific libraries have provided a useful tool for the further characterization of the Ashbya genome including positional cloning and genome sequencing.

• Molecules and Cells
• /
• v.20 no.3
• /
• pp.385-391
• /
• 2005

As a first step towards identifying genes involving in the signal transduction pathways mediating rice blast resistance, we isolated 3 mutants lines that showed enhanced susceptibility to rice blast KJ105 (91-033) from a T-DNA insertion library of the japonica rice cultivar, Hwayeong. Since none of the susceptible phenotypes co-segregated with the T-DNA insertion we adapted a map-based cloning strategy to isolate the gene(s) responsible for the enhanced susceptibility of the Hwayeong mutants. A genetic mapping population was produced by crossing the resistant wild type Hwayeong with the susceptible cultivar, Nagdong. Chi-square analysis of the $F_2$ segregating population indicated that resistance in Hwayeong was controlled by a single major gene that we tentatively named Pi-hy. Randomly selected susceptible plants in the $F_2$ population were used to build an initial map of Pi-hy. The SSLP marker RM2265 on chromosome 2 was closely linked to resistance. High resolution mapping using 105 $F_2$ plants revealed that the resistance gene was tightly linked, or identical, to Pib, a resistance gene with a nucleotide binding sequence and leucine-rich repeats (NB-LRR) previously isolated. Sequence analysis of the Pib locus amplified from three susceptible mutants revealed lesions within this gene, demonstrating that the Pi-hy gene is Pib. The Pib mutations in 1D-22-10-13, 1D-54-16-8, and 1C-143-16-1 were, respectively, a missense mutation in the conserved NB domain 3, a nonsense mutation in the 5th LRR, and a nonsense mutation in the C terminus following the LRRs that causes a small deletion of the C terminus. These findings provide evidence that NB domain 3 and the C terminus are required for full activity of the plant R gene. They also suggest that alterations of the resistance gene can cause major differences in pathogen specificity by affecting interactions with an avirulence factor.

• The KIPS Transactions:PartA
• /
• v.16A no.3
• /
• pp.143-152
• /
• 2009

One of the main issues in comparative genomics is to study chromosomal gene order in one or more related species. For this purpose, the whole genome alignment is usually applied to find the horizontal gene transfer, gene duplication, and gene loss between two related genomes. Also it is well known that the novel visualization tool with whole genome alignment is greatly useful for us to understand genome organization and evolution process. There are a lot of algorithms and visualization tools already proposed to find the "gene clusters" on genome alignments. But due to the huge size of whole genome, the previous visualization tools are not convenient to discover the relationship between two genomes. In this paper, we propose AlignScope, a novel visualization system for whole genome alignment, especially useful to find gene clusters between two aligned genomes. This AlignScope not only provides the simplified structure of genome alignment at any simplified level, but also helps us to find gene clusters. In experiment, we show the performance of AlignScope with several microbial genomes such as B. subtilis, B.halodurans, E. coli K12, and M. tuberculosis H37Rv, which have more than 5000 alignment pairs (matched DNA subsequence).

• Proceedings of the Korean Society of Potoscience Conference
• /
• spring
• /
• pp.77-85
• /
• 2003

• 대한생식의학회:학술대회논문집
• /
• 1999.11a
• /
• pp.106-106
• /
• 1999

• Proceedings of the Zoological Society Korea Conference
• /
• 1999.10b
• /
• pp.284.2-284
• /
• 1999

No Abstract, See Full Text

• The Plant Pathology Journal
• /
• v.19 no.1
• /
• pp.19-23
• /
• 2003

Turnip crinkle vims (TCV) inoculation onto resistant Arabidopsis ecotype Dijon（Di-17) leads to a hypersensitive response (HR) on the inoculated leaves. A dominant gene, HRT, which confers an HR to TCV, has been cloned from Di-17 plants by map-based cloning. HRT is a LZ-NBS-LRR class resistance gene and it belongs to a small gene family that includes RPP8, which confers resistance to Peronospora parasitica Emco5. Outside of the LRR region, HRT and RPP8 proteins share 98% amino acid identity while their LRR regions are less conserved (87% identity). HRT-transformed Arabidopsis plants developed an HR but generally remained susceptible to TCV due to a dominant RRT allele, which is not compatible with resistance. However, several transgenic plants that over-expressed HRT much higher than Di-l7 showed micro-HR or no HR when inoculated with TCV and were resistant to infection. Both the HR and resistance are dependent on salicylic acid but independent of NPRI, ethylene, or jasmonic acid. Arabidopsis plants containing both TCV coat protein gene and HRT developed massive necrosis and death in seedlings, indicating that the TCV coat protein is an avirulence factor detected by the HRT.

• Communications for Statistical Applications and Methods
• /
• v.29 no.1
• /
• pp.65-83
• /
• 2022

Although various statistical methods have been developed to map time-dependent genetic factors, most identified genetic variants can explain only a small portion of the estimated genetic variation in longitudinal traits. Gene-gene and gene-time/environment interactions are known to be important putative sources of the missing heritability. However, mapping epistatic gene-gene interactions is extremely difficult due to the very large parameter spaces for models containing such interactions. In this paper, we develop a Gaussian process (GP) based nonparametric Bayesian variable selection method for longitudinal data. It maps multiple genetic markers without restricting to pairwise interactions. Rather than modeling each main and interaction term explicitly, the GP model measures the importance of each marker, regardless of whether it is mostly due to a main effect or some interaction effect(s), via an unspecified function. To improve the flexibility of the GP model, we propose a novel grid-based method for the within-subject dependence structure. The proposed method can accurately approximate complex covariance structures. The dimension of the covariance matrix depends only on the number of fixed grid points although each subject may have different numbers of measurements at different time points. The deviance information criterion (DIC) and the Bayesian predictive information criterion (BPIC) are proposed for selecting an optimal number of grid points. To efficiently draw posterior samples, we combine a hybrid Monte Carlo method with a partially collapsed Gibbs (PCG) sampler. We apply the proposed GP model to a mouse dataset on age-related body weight.

• Asian Pacific Journal of Cancer Prevention
• /
• v.17 no.5
• /
• pp.2519-2525
• /
• 2016

There are several existing reports of microarray chip use for assessment of altered gene expression in different diseases. In fact, there have been over 1.5 million assays of this kind performed over the last twenty years, which have influenced clinical and translational research studies. The most commonly used DNA microarray platforms are Affymetrix GeneChip and Quality Control Software along with their GeneChip Probe Arrays. These chips are created using several quality controls to confirm the success of each assay, but their actual impact on gene expression profiles had not been previously analyzed until the appearance of several bioinformatics tools for this purpose. We here performed a data mining analysis, in this case specifically focused on ovarian cancer, as well as healthy ovarian tissue and ovarian cell lines, in order to confirm quality control results and associated variation in gene expression profiles. The microarray data used in our research were downloaded from ArrayExpress and Gene Expression Omnibus (GEO) and analyzed with Expression Console Software using RMA, MAS5 and Plier algorithms. The gene expression profiles were obtained using Partek Genomics Suite v6.6 and data were visualized using principal component analysis, heat map, and Venn diagrams. Microarray quality control analysis showed that roughly 40% of the microarray files were false negative, demonstrating over- and under-estimation of expressed genes. Additionally, we confirmed the results performing second analysis using independent samples. About 70% of the significant expressed genes were correlated in both analyses. These results demonstrate the importance of appropriate microarray processing to obtain a reliable gene expression profile.

• Proceedings of the Korean Society of Crop Science Conference
• /
• 2022.10a
• /
• pp.201-201
• /
• 2022

Rice bakanae disease is a serious global threat in major rice-cultivating regions worldwide causing high yield loss. It is caused by the fungal pathogen Fusarium fujikuroi. Varying degree of resistance or susceptibility to bakanae disease had been reported among Korean japonica rice varieties. We developed a modified in vitro bakanae disease bioassay method and tested 31 Korean japonica rice varieties. Nampyeong and Samgwang varieties showed highest resistance while 14 varieties including Junam and Hopum were highly susceptible with 100% mortality rate. We carried out mapping QTLs for bakanae disease resistance with four F2:F3 populations derived from the crosses between Korean japonica rice varieties. The Kompetitive Allele-Specific PCR (KASP) markers developed in our laboratory based on the SNPs detected in Korean japonica rice varieties were used in genotyping F2 plants in the populations. We found four major QTLs on chromosome 1, 4, 6, and 9 with LOD scores of 21.4, 6.9, 6.0, and 60.3, respectively. In addition, we are doing map-based cloning of the QTLs on chromosome 1 and 9 which were found with Junam/Nampyeong F2:F3 population and Junam/Samgwang F2:F3 population, respectively. These QTLs will be very useful in developing bakanae disease resistant high quality rice varieties.