• Proceedings of the Plant Resources Society of Korea Conference
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• 2020.08a
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• pp.49-49
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• 2020

Bacterial leaf blight (BLB), caused by X. oryzae pv. oryzae(Xoo), is one of the most destructive diseases of rice due to its high epidemic potential. Understanding BLB resistance at a genetic level is important to further improve the rice breeding that provides one of the best approaches to control BLB disease. In the present investigation, a total of 10,000 accessions of rice germplasm were tested to resistance degree of four Korean isolated races (K1, K2, K3 and K3a) of Xoo by bioassay and a diverse 268 accessions was selected to the genome-wide association study (GWAS) using high quality 34,724 SNPs to identify the associated with resistance loci. LOC_Os04g53160 of chromosome 4 was significantly associated with K1 race resistant. LOC_Os11g46230 and LOC_Os11g47150 of chromosome 11 were highly associated with K2 and K3 races as 23.7 and 27.4 of -log(P) value, but K3a resistant loci was weakly associated at LOC_Os03g55270 of chromosome 3. The results of the GWAS validate known gene of BLB resistant and identified novel loci of R genes that provide useful targets for further investigation to help the breeding system and identified gene and QTL provide valuable sources for further functional characterization.

• Molecules and Cells
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• v.26 no.6
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• pp.566-575
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• 2008

Twenty-five chipmunk species occur in the world, of which only the Siberian chipmunk, Tamias sibiricus, inhabits Asia. To investigate mitochondrial cytochrome b sequence variations and population structure of the Siberian chipmunk in northeastern Asia, we examined mitochondrial cytochrome b sequences (1140 bp) from 3 countries. Analyses of 41 individuals from South Korea and 33 individuals from Russia and northeast China resulted in 37 haplotypes and 27 haplotypes, respectively. There were no shared haplotypes between South Korea and Russia - northeast China. Phylogenetic trees and network analysis showed 2 major maternal lineages for haplotypes, referred to as the S and R lineages. Haplotype grouping in each cluster was nearly coincident with its geographic affinity. In particular, 3 distinct groups were found that mostly clustered in the northern, central and southern parts of South Korea. Nucleotide diversity of the S lineage was twice that of lineage R. The divergence between S and R lineages was estimated to be 2.98-0.98 Myr. During the ice age, there may have been at least 2 refuges in South Korea and Russia - northeast China. The sequence variation between the S and R lineages was 11.3% (K2P), which is indicative of specific recognition in rodents. These results suggest that T. sibiricus from South Korea could be considered a separate species. However, additional information, such as details of distribution, nuclear genes data or morphology, is required to strengthen this hypothesis.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.11
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• pp.1551-1557
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• 2015

The missing heritability has been a major problem in the analysis of best linear unbiased prediction (BLUP). We introduced the traditional genome-wide association study (GWAS) into the BLUP to improve the heritability estimation. We analyzed eight pork quality traits of the Berkshire breeds using GWAS and BLUP. GWAS detects the putative quantitative trait loci regions given traits. The single nucleotide polymorphisms (SNPs) were obtained using GWAS results with p value <0.01. BLUP analyzed with significant SNPs was much more accurate than that with total genotyped SNPs in terms of narrow-sense heritability. It implies that genomic estimated breeding values (GEBVs) of pork quality traits can be calculated by BLUP via GWAS. The GWAS model was the linear regression using PLINK and BLUP model was the G-BLUP and SNP-GBLUP. The SNP-GBLUP uses SNP-SNP relationship matrix. The BLUP analysis using preprocessing of GWAS can be one of the possible alternatives of solving the missing heritability problem and it can provide alternative BLUP method which can find more accurate GEBVs.

• Molecules and Cells
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• v.40 no.11
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• pp.823-827
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• 2017

Genome editing using programmable nucleases such as CRISPR/Cas9 or Cpf1 has emerged as powerful tools for gene knock-out or knock-in in various organisms. While most genetic diseases are caused by point mutations, these genome-editing approaches are inefficient in inducing single-nucleotide substitutions. Recently, Cas9-linked cytidine deaminases, named base editors (BEs), have been shown to convert cytidine to uridine efficiently, leading to targeted single-base pair substitutions in human cells and organisms. Here, we first report on the generation of Xenopus laevis mutants with targeted single-base pair substitutions using this RNA-guided programmable deaminase. Injection of base editor 3 (BE3) ribonucleoprotein targeting the tyrosinase (tyr) gene in early embryos can induce site-specific base conversions with the rates of up to 20.5%, resulting in oculocutaneous albinism phenotypes without off-target mutations. We further test this base-editing system by targeting the tp53 gene with the result that the expected single-base pair substitutions are observed at the target site. Collectively, these data establish that the programmable deaminases are efficient tools for creating targeted point mutations for human disease modeling in Xenopus.

• Genomics & Informatics
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• v.12 no.1
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• pp.42-47
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• 2014

Asian populations contain a variety of ethnic groups that have ethnically specific genetic differences. Ethnic variants may be highly relevant in disease and human differentiation studies. Here, we identified ethnically specific variants and then investigated their distribution across Asian ethnic groups. We obtained 58,960 Pan-Asian single nucleotide polymorphisms of 1,953 individuals from 72 ethnic groups of 11 Asian countries. We selected 9,306 ethnic variant single nucleotide polymorphisms (ESNPs) and 5,167 ethnic variant copy number polymorphisms (ECNPs) using the nearest shrunken centroid method. We analyzed ESNPs and ECNPs in 3 hierarchical levels: superpopulation, subpopulation, and ethnic population. We also identified ESNP- and ECNP-related genes and their features. This study represents the first attempt to identify Asian ESNP and ECNP markers, which can be used to identify genetic differences and predict disease susceptibility and drug effectiveness in Asian ethnic populations.

• Animal Systematics, Evolution and Diversity
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• v.24 no.1
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• pp.25-32
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• 2008

The Gold-spotted pond frog, Rana plancyi chosenica, designated as a vulnerable species by IUCN Red list. This species is a typical example facing local population threats and extinction due to human activities in South Korea. A strategic conservation plan for this endangered species is urgently needed. In order to provide information for future conservation planning, accurate information on the genetic diversity and taxonomic status is needed for the establishment of conservation units for this species. In this study, we used a molecular genetic approach using the mitochondrial cytochrome b gene and control region sequences to find the genetic diversity of gold-spotted pond frogs within South Korea. We sequenced the mitochondrial DNA cytochrome b gene and control region of 77 individuals from 11 populations in South Korea, and one from Chongqing, China. A total of 15 cytochrome b gene haplotypes and 34 control region haplotypes were identified from Korean gold-spotted pond frogs. Mean sequence diversity among Korean gold-spotted pond frogs was 0.31% (0.0-0.8%) and 0.51% (0.0-1.0%), respectively. Most Korean populations had at least one unique haplotype for each locus. The Taean, Ansan and Cheongwon populations had no haplotypes shared with other populations. There was a sequence divergence between Korean and Chinese gold-spotted pond frogs (1.3% for cyt b; 2.9% for control region). Analysis of genetic distances and phylogenetic trees based on both cytochrome b and control region sequences indicate that the Korean gold-spotted pond frog are genetically differentiated from those in China.

• Journal of Microbiology and Biotechnology
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• v.10 no.6
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• pp.873-876
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• 2000

Short tendem repeat (STR) loci have been used in the field of forensic science. There are literally hundreds of STR systems which have been mapped throughout the human genome. These STR loci are found in almost every chromosome in the genome. They may be amplified using a variety of PCR primers. In this study, a DNA genotyping system based on the multiplex amplification of highly polymorphic STR loci was developed. Three STR loci with nonoverlapping allele size ranges have been utilized in the multiplex amplification including the Neurotensin receptor gene, D21S11, and Human tyrosine hydroxylase gene. The optimal condition for triplex PCr was obtained in a solution with a total volume of $25{\mu}l$ containing 2.0 U of Taq polymerase, 3 mM of $MgCl_2$, $300{\mu}M$ of dNTP, 10 pmole of each primer set, an annealing temperature of $62^{\circ}C$, and 35 cycles. The optimized condition was successfully employed in a family paternity test.

• Korean Journal of Clinical Laboratory Science
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• v.38 no.2
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• pp.99-104
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• 2006

Human Papilloma viruses (HPVs) are etiological agents for cervical cancer and are classified into low- and high-risk categories. The aim of this study was to determine the frequency of the HPV genotype in the HPV screening test of Korean women using PCR-direct sequencing. Consensus primers of L1 legion were used for the amplification of HPV DNA and the PCR products (450 bps) obtained were analyzed by automatic sequencing. Sequences were compared with those in GenBank by using the BLAST program. Cervical swab samples of 3,978 women (20-73 years) were tested and the average age was 37.6 years. In this study, 1,174 samples were HPV positive out of 3,978 cervical swab samples screened (29.5%) and 136 samples (11.6%) showed a double infection. A total of 1,310 HPV genotypes were analyzed. The HPV positive rate was the lowest in the 20 years group (69.5%) and most of the samples of the > 60 years group were found HPV positive. Among thirty seven different HPV types identified by sequencing, 21 were HPV high risk types and 16 HPV low risk types were 69.8% (914/1,310) and 26.0% (340/1,310), respectively. In HPV high-risk types, 16 (13.21%), was the most frequently found. HPV 53 (9.62%) and 58 (9.24%) were also frequently found. This group was followed by HPV types 70 (5.50%), 33 (4.73%), 66 (4.20%), 18 (4.05%), 52 (4.05%), 31 (3.97%) and 56 (3.51%) in descending order of frequency. Among HPV low-risk types, 62 (4.20%), 6 (3.59%), 81 (3.59%), 84 (3.51%), and 11 (2.6%) were frequently found. In conclusion, PCR-direct sequencing could be used for quick and reliable typing of known and novel HPVs from clinical specimens. This data could be useful for epidemiological study of HPV and it also allows type-specific follow-up of women who have been treated for cervical intraepithelial neoplasia.

• Journal of Plant Biotechnology
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• v.35 no.4
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• pp.265-274
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• 2008

Glutathione S-transferases (GSTs) are multifunctional proteins encoded by a large gene family divided into Phi, Tau, Theta, Zeta, Lambda and DHAR classes on the basis of sequence identity. The Phi(F) and Tau(U) classes are plant-specific and ubiquitous. Their roles have been defined as herbicide detoxification and responses to biotic and abiotic stresses. Fifty-two members of the GST super-family were identified in the Arabidopsis thaliana genome, 13 members of which belong to the Phi class of GSTs (AtGSTFs). Based on the sequence similarities of AtGSTFs, 11 BAC clones were identified from Brassica rapa. Seven unique sequences of ORFs designated the Phi class candidates of GST derived from B. rapa (BrGSTFs) were detected from these 11 BAC clones by blast search and sequence alignment. Some of BrGSTFs were present in the same BAC clones indicating that BrGSTFs could also be clustered as usual in plant. They were mapped on B. rapa linkage group 2, 3, 9 and 10 and their nucleotide and amino acid sequences were highly similar to those of AtGSTFs. In addition, in silico analysis of BrGSTFs using Korea Brassica Genome Project 24K oligochip and microarray database for cold, salt and drought stresses revealed 15 unigenes to be highly similar to AtGSTFs and six of these were identical to one of BrGSTFs identified in the BAC clones indicating their expression. The sequences of BrGSTFs and unigenes identified in this study will facilitate further studies to apply GST genes to medical and agriculture purposes.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.2
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• pp.166-170
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• 2015

Foot-and-mouth disease (FMD) is a highly contagious disease affecting cloven-hoofed animals and causes severe economic loss and devastating effect on international trade of animal or animal products. Since FMD outbreaks have recently occurred in some Asian countries, it is important to understand the relationship between diverse immunogenomic structures of host animals and the immunity to foot-and-mouth disease virus (FMDV). We performed genome wide association study based on high-density bovine single nucleotide polymorphism (SNP) chip for identifying FMD resistant loci in Holstein cattle. Among 624532 SNP after quality control, we found that 11 SNPs on 3 chromosomes (chr17, 22, and 15) were significantly associated with the trait at the p.adjust <0.05 after PERMORY test. Most significantly associated SNPs were located on chromosome 17, around the genes Myosin XVIIIB and Seizure related 6 homolog (mouse)-like, which were associated with lung cancer. Based on the known function of the genes nearby the significant SNPs, the FMD resistant animals might have ability to improve their innate immune response to FMDV infection.