• Korean Journal of Agricultural Science
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• v.43 no.1
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• pp.1-13
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• 2016

Climate changes are shifting the perception of C4 photosynthetic crops due to their superior adaptability to harsh conditions. The tribe Andropogoneae includes some economically important grasses, such as Zea mays, Sorghum bicolor, Miscanthus spp., and Saccharum spp., representing C4 photosynthetic grasses. Although the Andropogoneae grasses diverged fairly recently, their genomic structures are remarkably different from each other. As previously reported, the family Poaceae shares the pan-cereal duplication event occurring ca. 65 MYA. Since this event, Sorghum bicolor has never experienced any additional duplication event. However, some lineage-specific duplication events were reported in Z. mays and Saccharum spp., and, more recently, it was revealed that a shared allotetraploidization event occurred before the divergence between Miscanthus and Saccharum (but after the divergence from S. bicolor), which provided important clues to those two species having large genome sizes with complicated ploidy numbers. The complex genomic structures of sugarcane and Miscanthus (defined as the Saccharum complex along with some other taxa) have had a limiting effect on the use of their molecular information in breeding programs. For the last decade, genomics-associated technologies have become an important tool for molecular crop breeding (genomics-assisted breeding, GAB), but it has not been directly applied to sugarcane and Miscanthus due to their complicated genome structures. As genomics research advances, molecular breeding of those crops can take advantage of technical improvements at a reasonable cost through comparative genomic approaches. Active genomic research of non-model species using closely related model species will facilitate the improvement of those crops in the future.

• Reproductive and Developmental Biology
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• v.29 no.1
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• pp.9-13
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• 2005

This study was performed to analyze the sequence variation in mtDNA D-loop and their effects on milk and milk fat production in Holstein cows. The analyzed sequences were compared with previously published sequences from other cattle breeds (GenBank J01394). PCR was performed to amplify a total of 964 bp between nucleotide 15758 and 383 within D-loop region of mtDNA using specific primers. Thirty five polymorphic sites by nucleotide substitution were found in mtDNA. The frequencies of positions at 106, 169, 16057, 16231 and 16255 nt with high levels of sequence polymorphism were 0.090, 0.555, 0.055, 0.090 and 0.050, respectively. The substitution effect at 169 nt was found significant on milk production, and substitution effect at 16118, 16139 and 16302 nt was highly significant (p<0.1) on milk fat production. Polymorphism of mtDNA sequence in D-loop region might be useful for the analysis of cytoplasmic genetic variation and associations with the other economically important traits and maternal lineage analysis in Holstein cows.

• Journal of Embryo Transfer
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• v.31 no.3
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• pp.243-247
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• 2016

Growth traits, such as body weight, directly influence productivity and economic efficiency in the swine industry. In this study, we estimate heritability for body weight traits usinginformation from pedigree and genome-wide single nucleotide polymorphism (SNP) chip data. Four body weight phenotypes were measured in 1,105 $F_2$ progeny from an intercross between Landrace and Jeju native black pigs. All experimental animals were subjected to genotypic analysis using PorcineSNP60K BeadChip platform, and 39,992 autosomal SNP markers filtered by quality control criteria were used to construct genomic relationship matrix for heritability estimation. Restricted maximum likelihood estimates of heritability were obtained using both genomic- and pedigree- relationship matrix in a linear mixed model. The heritability estimates using SNP information were smaller (0.36-0.55) than those which were estimated using pedigree information (0.62-0.97). To investigate effect of common environment, such as maternal effect, on heritability estimation, we included maternal effect as an additional random effect term in the linear mixed model analysis. We detected substantial proportions of phenotypic variance components were explained by maternal effect. And the heritability estimates using both pedigree and SNP information were decreased. Therefore, heritability estimates must be interpreted cautiously when there are obvious common environmental variance components.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.12
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• pp.1836-1843
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• 2019

Objective: Social genetic effects (SGE) are an important genetic component for growth, group productivity, and welfare in pigs. The present study was conducted to evaluate i) the feasibility of the single-step genomic best linear unbiased prediction (ssGBLUP) approach with the inclusion of SGE in the model in pigs, and ii) the changes in the contribution of heritable SGE to the phenotypic variance with different scaling ${\omega}$ constants for genomic relationships. Methods: The dataset included performance tested growth rate records (average daily gain) from 13,166 and 21,762 pigs Landrace (LR) and Yorkshire (YS), respectively. A total of 1,041 (LR) and 964 (YS) pigs were genotyped using the Illumina PorcineSNP60 v2 BeadChip panel. With the BLUPF90 software package, genetic parameters were estimated using a modified animal model for competitive traits. Giving a fixed weight to pedigree relationships (${\tau}:1$), several weights (${\omega}_{xx}$, 0.1 to 1.0; with a 0.1 interval) were scaled with the genomic relationship for best model fit with Akaike information criterion (AIC). Results: The genetic variances and total heritability estimates ($T^2$) were mostly higher with ssGBLUP than in the pedigree-based analysis. The model AIC value increased with any level of ${\omega}$ other than 0.6 and 0.5 in LR and YS, respectively, indicating the worse fit of those models. The theoretical accuracies of direct and social breeding value were increased by decreasing ${\omega}$ in both breeds, indicating the better accuracy of ${\omega}_{0.1}$ models. Therefore, the optimal values of ${\omega}$ to minimize AIC and to increase theoretical accuracy were 0.6 in LR and 0.5 in YS. Conclusion: In conclusion, single-step ssGBLUP model fitting SGE showed significant improvement in accuracy compared with the pedigree-based analysis method; therefore, it could be implemented in a pig population for genomic selection based on SGE, especially in South Korean populations, with appropriate further adjustment of tuning parameters for relationship matrices.

• Information Systems Review
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• v.23 no.3
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• pp.97-125
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• 2021

Blockchain is a core technology to solve personal information leakage and data management issues, which are limitations of existing Genomic Sequencing services. Due to continuous cost reduction and deregulation, the market size of Genomic Sequencing has been increasing, also the potential of services is expected to increase when Blockchain's security and connectivity are combined. We created our research model by combining the Technology Acceptance Model (TAM) and the Innovation Resistance Theory also analyzed the factors affecting the acceptance intention and innovation resistance of the Blockchain Based Genomic Sequencing Information Platform. A survey was conducted on 150 potential users of Blockchain and Genomic Sequencing services. The analysis was conducted by setting the four Blockchain variables: Security, transparency, availability, and diversity). Also, we set the Perceived Usefulness, Perceived risk, and Perceived Complexity for Technology Acceptance and Innovation Resistance variables and analyzed the effect of the characteristics of the Blockchain on acceptance intention and innovation resistance through these variables. Through this analysis, key variables that need to be considered important to reduce resistance and increase acceptance intention could be identified. This study presents innovation factors that should be considered in companies preparing a new Blockchain Based Genomic Sequencing Information Platform.

• Korean Journal of Poultry Science
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• v.40 no.2
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• pp.83-89
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• 2013

iNOS (Inducible nitric oxide synthase) and TLR-4 (Toll-like Receptor-4) play crucial roles in innate immunity of poultry. iNOS has been mapped to chicken chromosome 14 and implicated in a variety of chicken diseases. iNOS possesses potent antimicrobial activity, including the inhibition of microbes replication in vitro. TLR-4 is a pathogen associated molecular-pattern receptor for bacterial product, such as LPS (lipopolysaccharides) found in Gram negative bacteria, that triggers pro-inflammatory cytokine expression after engagement with ligands. In the previous studies, genetic analysis of iNOS and TLR-4 revealed the possible association of mutation in these genes with the intestinal microflora of cecum when infected with Salmonella spp. This study was aimed to augment previous findings, which show the association of iNOS (C14513T) and TLR-4 (G4409T) polymorphisms with economic traits in Korean Native Black (KNB), Rhode Island Red (RIR) and Cornish chickens. Investigation in the effect of SNPs on economic traits (layday, layw, layno, bw150, bw270, layw270) was conducted. iNOS (C14513T) had a significant effect on the average body weight at 270 days of age (p<0.05) in both KNB and RIR, whereas TLR-4 (G4409T) showed no significant correlation with all traits (p>0.05). The results obtained from using the candidate genes can be useful for the genetic improvement of body weight in both KNB and RIR breeds.

• Korean Journal of Poultry Science
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• v.40 no.2
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• pp.115-120
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• 2013

Thyroid hormone (TH) plays a role in growth of the poultry. Thyroid-stimulating hormone (TSH) stimulates production and distribution of TH, and is a heterodimer which is formed by ${\alpha}$- and ${\beta}$-subunits. Most of TSH activity is known to rely on ${\beta}$-subunit. TSH-${\beta}$ gene is located on chicken chromosome 26 and associated with growth performances. Therefore, this study aimed to investigate the association of TSH- ${\beta}$ SNP (G1031C) with economic traits (layday, layw, layno, bw150, bw270, layw270) in Korean Native Black chicken, Rhode Island Red and Cornish. Allele frequency of GG genotype in Rhode Island Red (RIR) was found to be 1.00 in this study. A significant effect was only observed on body weight at day 150 in Cornish. In Cornish, body weights of chicken with the CC genotype ($302.15{\pm}6.336$) were significantly higher than that of the GG genotype ($294.56{\pm}4.537$) (p<0.05). These findings suggest that the G1031C SNP of TSH-${\beta}$ gene can be used for improvement of growth-related traits in Cornish.

• BMB Reports
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• v.36 no.4
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• pp.403-408
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• 2003

The relative activities of neutral, cationic, and anionic chromium ascorbate complexes toward isolated human mitochondrial and genomic DNA were investigated at physiologically relevant conditions by agarose gel electrophoresis. A direct relationship between the charge of the Cr(III) species and their DNA-damaging properties was found. The cationic species were found to be fully capable of DNA-cleavage, even in short incubation periods. Incubations were also performed in the presence of amino acids. No apparent effect was observed under the applied experimental conditions to facilitate or prevent damage through the ternary amino acid-Cr-DNA adduct formation or binary chromium-amino acid complex formation.

• Genomics & Informatics
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• v.16 no.4
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• pp.27.1-27.6
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• 2018

The non-coding DNA in eukaryotic genomes encodes a language that programs chromatin accessibility, transcription factor binding, and various other activities. The objective of this study was to determine the effect of the primary DNA sequence on the epigenomic landscape across a 200-base pair of genomic units by integrating 127 publicly available ChromHMM BED files from the Roadmap Genomics project. Nucleotide frequency profiles of 127 chromatin annotations stratified by chromatin variability were analyzed and integrative hidden Markov models were built to detect Markov properties of chromatin regions. Our aim was to identify the relationship between DNA sequence units and their chromatin variability based on integrated ChromHMM datasets of different cell and tissue types.

• Genomics & Informatics
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• v.21 no.2
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• pp.27.1-27.7
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• 2023

Recombination events complicate the evolutionary history of populations and species and have a significant impact on the inference of isolation-with-migration (IM) models. However, several existing methods have been developed, assuming no recombination within a locus and free recombination between loci. In this study, we investigated the effect of recombination on the estimation of IM models using genomic data. We conducted a simulation study to evaluate the consistency of the parameter estimators with up to 1,000 loci and analyze true gene trees to examine the sources of errors in estimating the IM model parameters. The results showed that the presence of recombination led to biased estimates of the IM model parameters, with population sizes being more overestimated and migration rates being more underestimated as the number of loci increased. The magnitude of the biases tended to increase with the recombination rates when using 100 or more loci. On the other hand, the estimation of splitting times remained consistent as the number of loci increased. In the absence of recombination, the estimators of the IM model parameters remained consistent.