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Dive into the research topics where Jae-Don Oh is active.

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Featured researches published by Jae-Don Oh.


PLOS ONE | 2014

Whole-genome analyses of Korean native and Holstein cattle breeds by massively parallel sequencing.

Jung-Woo Choi; Xiaoping Liao; Paul Stothard; Won-Hyong Chung; Heoyn-Jeong Jeon; Stephen P. Miller; So-Young Choi; Jeong-Koo Lee; Bokyoung Yang; Kyung-Tai Lee; Kwang-Jin Han; Hyeong-Cheol Kim; Dongkee Jeong; Jae-Don Oh; Namshin Kim; Tae-Hun Kim; Hak-Kyo Lee; Sung Jin Lee

A main goal of cattle genomics is to identify DNA differences that account for variations in economically important traits. In this study, we performed whole-genome analyses of three important cattle breeds in Korea—Hanwoo, Jeju Heugu, and Korean Holstein—using the Illumina HiSeq 2000 sequencing platform. We achieved 25.5-, 29.6-, and 29.5-fold coverage of the Hanwoo, Jeju Heugu, and Korean Holstein genomes, respectively, and identified a total of 10.4 million single nucleotide polymorphisms (SNPs), of which 54.12% were found to be novel. We also detected 1,063,267 insertions–deletions (InDels) across the genomes (78.92% novel). Annotations of the datasets identified a total of 31,503 nonsynonymous SNPs and 859 frameshift InDels that could affect phenotypic variations in traits of interest. Furthermore, genome-wide copy number variation regions (CNVRs) were detected by comparing the Hanwoo, Jeju Heugu, and previously published Chikso genomes against that of Korean Holstein. A total of 992, 284, and 1881 CNVRs, respectively, were detected throughout the genome. Moreover, 53, 65, 45, and 82 putative regions of homozygosity (ROH) were identified in Hanwoo, Jeju Heugu, Chikso, and Korean Holstein respectively. The results of this study provide a valuable foundation for further investigations to dissect the molecular mechanisms underlying variation in economically important traits in cattle and to develop genetic markers for use in cattle breeding.


Molecules and Cells | 2013

Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels.

Jung-Woo Choi; Xiaoping Liao; Sairom Park; Heoyn-Jeong Jeon; Won-Hyong Chung; Paul Stothard; Yeon-Soo Park; Jeong-Koo Lee; Kyung-Tai Lee; Sang-Hwan Kim; Jae-Don Oh; Namshin Kim; Tae-Hun Kim; Hak-Kyo Lee; Sung Jin Lee

Since the completion of the bovine sequencing projects, a substantial number of genetic variations such as single nucleotide polymorphisms have become available across the cattle genome. Recently, cataloguing such genetic variations has been accelerated using massively parallel sequencing technology. However, most of the recent studies have been concentrated on European Bos taurus cattle breeds, resulting in a severe lack of knowledge for valuable native cattle genetic resources worldwide. Here, we present the first whole-genome sequencing results for an endangered Korean native cattle breed, Chikso, using the Illumina HiSeq 2,000 sequencing platform. The genome of a Chikso bull was sequenced to approximately 25.3-fold coverage with 98.8% of the bovine reference genome sequence (UMD 3.1) covered. In total, 5,874,026 single nucleotide polymorphisms and 551,363 insertion/deletions were identified across all 29 autosomes and the X-chromosome, of which 45% and 75% were previously unknown, respectively. Most of the variations (92.7% of single nucleotide polymorphisms and 92.9% of insertion/deletions) were located in intergenic and intron regions. A total of 16,273 single nucleotide polymorphisms causing missense mutations were detected in 7,111 genes throughout the genome, which could potentially contribute to variation in economically important traits in Chikso. This study provides a valuable resource for further investigations of the genetic mechanisms underlying traits of interest in cattle, and for the development of improved genomics-based breeding tools.


International Journal of Nanomedicine | 2014

Virgin olive oil blended polyurethane micro/nanofibers ornamented with copper oxide nanocrystals for biomedical applications

Touseef Amna; M. Shamshi Hassan; Jieun Yang; Myung-Seob Khil; Ki-Duk Song; Jae-Don Oh; Inho Hwang

Recently, substantial interest has been generated in using electrospun biomimetic nanofibers of hybrids, particularly organic/inorganic, to engineer different tissues. The present work, for the first time, introduced a unique natural and synthetic hybrid micronanofiber wound dressing, composed of virgin olive oil/copper oxide nanocrystals and polyurethane (PU), developed via facile electrospinning. The as-spun organic/inorganic hybrid micronanofibers were characterized by scanning electron microscopy (SEM), energy dispersive X-ray analysis, X-ray diffraction, electron probe microanalysis, and transmission electron microscopy. The interaction of cells with scaffold was studied by culturing NIH 3T3 fibroblasts on an as-spun hybrid micronanofibrous mat, and viability, proliferation, and growth were assessed. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay results and SEM observation showed that the hybrid micronanofibrous scaffold was noncytotoxic to fibroblast cell culture and was found to benefit cell attachment and proliferation. Hence our results suggest the potential utilization of as-spun micronanoscaffolds for tissue engineering. Copper oxide–olive oil/PU wound dressing may exert its positive beneficial effects at every stage during wound-healing progression, and these micronanofibers may serve diverse biomedical applications, such as tissue regeneration, damaged skin treatment, wound healing applications, etc. Conclusively, the fabricated olive oil–copper oxide/PU micronanofibers combine the benefits of virgin olive oil and copper oxide, and therefore hold great promise for biomedical applications in the near future.


Poultry Science | 2014

Differential regulation of microRNA transcriptome in chicken lines resistant and susceptible to necrotic enteritis disease

Yeong Ho Hong; Hue Dinh; Hyun S. Lillehoj; Ki-Duk Song; Jae-Don Oh

Necrotic enteritis (NE) is a re-emerging disease as a result of increased restriction on the use of antibiotics in poultry. However, the molecular mechanisms underlying the pathogenesis of NE are unclear. Small RNA transcriptome analysis was performed using spleen and intestinal intraepithelial lymphocytes (IEL) from 2 inbred chicken lines selected for resistance or susceptibility to Mareks disease (MD) in an experimentally induced model of avian NE to investigate whether microRNA (miRNA) control the expression of genes associated with host response to pathogen challenge. Unique miRNA represented only 0.02 to 0.04% of the total number of sequences obtained, of which 544 were unambiguously identified. Hierarchical clustering revealed that most of miRNA in IEL were highly expressed in the MD-susceptible line 7.2 compared with MD-resistant line 6.3. Reduced CXCL14 gene expression was correlated with differential expression of several unique miRNA in MD-resistant chickens, whereas TGFβR2 gene expression was correlated with altered gga-miR-216 miRNA levels in MD-susceptible animals. In conclusion, miRNA profiling and deep sequencing of small RNA in experimental models of infectious diseases may be useful for further understanding of host-pathogen interactions, and for providing insights into genetic markers of disease resistance.


Functional & Integrative Genomics | 2014

Antimicrobial peptides in the centipede Scolopendra subspinipes mutilans

Won Gi Yoo; Joon Ha Lee; Younhee Shin; Jaeyoung Shim; Myunghee Jung; Byeong-Chul Kang; Jae-Don Oh; Jiyeon Seong; Hak Kyo Lee; Hong Sik Kong; Ki-Duk Song; Eun-Young Yun; In-Woo Kim; Young-Nam Kwon; Dong Gun Lee; Ui-Wook Hwang; Junhyung Park; Jae Sam Hwang

The centipede Scolopendra subspinipes mutilans is an environmentally beneficial and medically important arthropod species. Although this species is increasingly applied as a reliable source of new antimicrobial peptides, the transcriptome of this species is a prerequisite for more rational selection of antimicrobial peptides. In this report, we isolated total RNA from the whole body of adult centipedes, S. subspinipes mutilans, that were nonimmunized and immunized against Escherichia coli, and we generated a total of 77,063 pooled contigs and singletons using high-throughput sequencing. To screen putative antimicrobial peptides, in silico analyses of the S. subspinipes mutilans transcriptome were performed based on the physicochemical evidence of length, charge, isoelectric point, and in vitro and in vivo aggregation scores together with the existence of continuous antimicrobial peptide stretches. Moreover, we excluded some transcripts that showed similarity with both previously known antimicrobial peptides and the human proteome, had a proteolytic cleavage site, and had downregulated expression compared with the nonimmunized sample. As a result, we selected 17 transcripts and tested their antimicrobial activity with a radial diffusion assay. Among them, ten synthetic peptides experimentally showed antimicrobial activity against microbes and no toxicity to mouse erythrocytes. Our results provide not only a useful set of antimicrobial peptide candidates and an efficient strategy for novel antimicrobial peptide development but also the transcriptome data of a big centipede as a valuable resource.


PLOS ONE | 2015

Exploring the Genetic Signature of Body Size in Yucatan Miniature Pig

Hyeongmin Kim; Ki Duk Song; Hyeon Jeong Kim; Woncheoul Park; Jaemin Kim; Taeheon Lee; Donghyun Shin; Woori Kwak; Young-jun Kwon; Samsun Sung; S. J. Moon; Kyung-Tai Lee; Namshin Kim; Joon Ki Hong; Kyung Yeon Eo; Kang Seok Seo; Girak Kim; Sung-Moo Park; Cheol-Heui Yun; Hyunil Kim; Kimyung Choi; Jiho Kim; Woon Kyu Lee; Duk-Kyung Kim; Jae-Don Oh; Eui-Soo Kim; Seoae Cho; Hak-Kyo Lee; Tae-Hun Kim; Heebal Kim

Since being domesticated about 10,000–12,000 years ago, domestic pigs (Sus scrofa domesticus) have been selected for traits of economic importance, in particular large body size. However, Yucatan miniature pigs have been selected for small body size to withstand high temperature environment and for laboratory use. This renders the Yucatan miniature pig a valuable model for understanding the evolution of body size. We investigate the genetic signature for selection of body size in the Yucatan miniature pig. Phylogenetic distance of Yucatan miniature pig was compared to other large swine breeds (Yorkshire, Landrace, Duroc and wild boar). By estimating the XP-EHH statistic using re-sequencing data derived from 70 pigs, we were able to unravel the signatures of selection of body size. We found that both selections at the level of organism, and at the cellular level have occurred. Selection at the higher levels include feed intake, regulation of body weight and increase in mass while selection at the molecular level includes cell cycle and cell proliferation. Positively selected genes probed by XP-EHH may provide insight into the docile character and innate immunity as well as body size of Yucatan miniature pig.


Asian-australasian Journal of Animal Sciences | 2014

Genetic Traceability of Black Pig Meats Using Microsatellite Markers

Jae-Don Oh; Ki-Duk Song; Joo-Hee Seo; Duk-Kyung Kim; Sung-Hoon Kim; Kang-Seok Seo; Hyun-Tae Lim; Jae-Bong Lee; Hwa-Chun Park; Youn-Chul Ryu; Min-Soo Kang; Seoae Cho; Eui-Soo Kim; Ho-Sung Choe; Hong-Sik Kong; Hak-Kyo Lee

Pork from Jeju black pig (population J) and Berkshire (population B) has a unique market share in Korea because of their high meat quality. Due to the high demand of this pork, traceability of the pork to its origin is becoming an important part of the consumer demand. To examine the feasibility of such a system, we aim to provide basic genetic information of the two black pig populations and assess the possibility of genetically distinguishing between the two breeds. Muscle samples were collected from slaughter houses in Jeju Island and Namwon, Chonbuk province, Korea, for populations J and B, respectively. In total 800 Jeju black pigs and 351 Berkshires were genotyped at thirteen microsatellite (MS) markers. Analyses on the genetic diversity of the two populations were carried out in the programs MS toolkit and FSTAT. The population structure of the two breeds was determined by a Bayesian clustering method implemented in structure and by a phylogenetic analysis in Phylip. Population J exhibited higher mean number of alleles, expected heterozygosity and observed heterozygosity value, and polymorphism information content, compared to population B. The FIS values of population J and population B were 0.03 and −0.005, respectively, indicating that little or no inbreeding has occurred. In addition, genetic structure analysis revealed the possibility of gene flow from population B to population J. The expected probability of identify value of the 13 MS markers was 9.87×10−14 in population J, 3.17×10−9 in population B, and 1.03×10−12 in the two populations. The results of this study are useful in distinguishing between the two black pig breeds and can be used as a foundation for further development of DNA markers.


BMC Genetics | 2015

Exploring evidence of positive selection reveals genetic basis of meat quality traits in Berkshire pigs through whole genome sequencing.

Hyeonsoo Jeong; Ki-Duk Song; Minseok Seo; Kelsey Caetano-Anolles; Jaemin Kim; Woori Kwak; Jae-Don Oh; Eui-Soo Kim; Dong Kee Jeong; Seoae Cho; Heebal Kim; Hak-Kyo Lee

BackgroundNatural and artificial selection following domestication has led to the existence of more than a hundred pig breeds, as well as incredible variation in phenotypic traits. Berkshire pigs are regarded as having superior meat quality compared to other breeds. As the meat production industry seeks selective breeding approaches to improve profitable traits such as meat quality, information about genetic determinants of these traits is in high demand. However, most of the studies have been performed using trained sensory panel analysis without investigating the underlying genetic factors. Here we investigate the relationship between genomic composition and this phenotypic trait by scanning for signatures of positive selection in whole-genome sequencing data.ResultsWe generated genomes of 10 Berkshire pigs at a total of 100.6 coverage depth, using the Illumina Hiseq2000 platform. Along with the genomes of 11 Landrace and 13 Yorkshire pigs, we identified genomic variants of 18.9 million SNVs and 3.4 million Indels in the mapped regions. We identified several associated genes related to lipid metabolism, intramuscular fatty acid deposition, and muscle fiber type which attribute to pork quality (TG, FABP1, AKIRIN2, GLP2R, TGFBR3, JPH3, ICAM2, and ERN1) by applying between population statistical tests (XP-EHH and XP-CLR). A statistical enrichment test was also conducted to detect breed specific genetic variation. In addition, de novo short sequence read assembly strategy identified several candidate genes (SLC25A14, IGF1, PI4KA, CACNA1A) as also contributing to lipid metabolism.ConclusionsResults revealed several candidate genes involved in Berkshire meat quality; most of these genes are involved in lipid metabolism and intramuscular fat deposition. These results can provide a basis for future research on the genomic characteristics of Berkshire pigs.


Korean Journal of Poultry Science | 2010

Comparison for genetic diversity between Korean native commercial chicken brand groups using microsatellite markers.

Hak-Kyo Lee; Jae-Don Oh; Chan-Ho Park; Kun-Woo Lee; Jun-Heon Lee; Gwang-Joo Jeon; Hong-Sik Kong

To estimate the genetic characteristics within two brands of Korean native commercial chicken, we used a total of 302 genomic DNAs from two groups (Woorichicken: 152, Hanhyup3chicken: 150). Sizes of 10 microsatellite markers were decided using GeneMapper Software (v.4.0) after analyzing ABI 3130. Genetic diversity indices including expected heterozygosity (Ex H), observed heterozygosity (Ob H) and polymorphism information content (PIC). Frequencies of microsatellites markers were used to estimate heterozygosities and genetic distances. LEI0073 showed the highest value in all genetic diversity (Ex H, Ob H and PIC). On the other hand, MCW322 showed the lowest value in all genetic diversity. The calculated genetic distance of the two brand groups is 0.199 (standard genetic distance) and 0.132 (DA distance). Genetic distances of the two groups were relatively


Korean Journal of Poultry Science | 2010

Estimation of genetic characteristic and cumulative power of discrimination using the microsatellite markers in Korean Native Chicken.

Kun-Woo Lee; Jae-Don Oh; Jin-Ah Lee; Kyu-Ho Cho; In-Sik Nam; Jun-Heon Lee; Ok-Suk Seo; Gwang-Joo Jeon; Hak-Kyo Lee; Hong-Sik Kong

To estimate the genetic characteristics and cumulative power of discrimination (CPD) Korean Native Chicken. We used a total of 195 genomic DNAs from four breeds population (Korean Native Red chicken: R, Korean Native Yellow chicken: Y, Korean Native Black chicken: L, Ogal chicken: S). Frequencies of microsatellites markers were used to estimate heterozygosities and genetic distances. The lowest distance (0.05) was observed between the R and L strains and the highest distance (0.158) between the L and S strains. Korean native chicken strains (R, Y, K) have each other comparatively near genetic distance. Cumulative power of discriminate (CPD) was 99.999% by including the 10 microsatellites loci individual identification system. And then matching probability in that two different individuals incidentally have same genotype was estimated to 0.36×10 -7 . The system employing

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Hak-Kyo Lee

Chonbuk National University

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Ki-Duk Song

Chonbuk National University

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Hong-Sik Kong

Hankyong National University

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Byung-Wook Cho

Pusan National University

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Kun-Woo Lee

Hankyong National University

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Kyung-Do Park

Hankyong National University

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Heebal Kim

Seoul National University

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Seoae Cho

Seoul National University

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Jun-Heon Lee

Chungnam National University

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Jaemin Kim

Seoul National University

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