• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.101-101
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• 2017

This study was carried out to improve yield potential of Tongil type rice variety based on QTLs analysis associated with yield component using a total of 386 rice recombinant inbred lines (RILs) derived from a cross between Tongil type high yield variety "Hanareum2" and Japonica variety "Unkwang". 384 SNP markers were used, and 241 of them (62.6%) were polymorphic between Hanareum2 and Unkwang. One hundred forty-four QTLs in 11 traits, such as heading days, were detected. Most of them were 21 QTLs associated with 1000 grain weight and the least was 8 QTLs associated with panicle number. The QTL, qDTH3-2 associated with days to heading was identified to delay heading date for 2.4~2.6 day. Eleven QTLs were associated with culm length. The QTL, qCL1-2 on chromosome 1, was identified to decrease culm length. A total of 16 QTLs were detected for panicle length. Three QTLs, qPL3, qPL6, and qPL7-1 were increased panicle length. Seven QTLs related to panicle number except qPN7 were increased the number of panicle. Four QTLs related to grain number per panicle, qGNP2-1, qGNP6, and qGNP7, were increased the number of grains. Three QTLs associated with grain filling rate, qGFR1, qGFR2-2, and qGFR7-1 were increased grain filling rate. Twelve QTLs associated with 1,000 grain weight. were increased the grain weight. Fourteen QTLs were identified associated with grain length. 10 QTLs, such as qGL1-1, were increasing grain. Fifteen QTLs associated with grain width were detected. The 8 QTLs, such as qGW1-1, were elongated grain width. Seventeen QTLs were associated with grain thickness, and ten QTLs of them were increased grain thickness. We need further study to develop introgression lines of each QTL to improve yield potential of Tongil type rice variety.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.10
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• pp.1565-1574
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• 2018

Objective: The aim of the present study was to identify genetic variants based on RNA-seq data, obtained via transcriptome sequencing of muscle tissue of pigs differing in muscle histological structure, and to verify the variants' effect on histological microstructure and production traits in a larger pig population. Methods: RNA-seq data was used to identify the panel of single nucleotide polymorphisms (SNPs) significantly related with percentage and diameter of each fiber type (I, IIA, IIB). Detected polymorphisms were mapped to quantitative trait loci (QTLs) regions. Next, the association study was performed on 944 animals representing five breeds (Landrace, Large White, Pietrain, Duroc, and native Puławska breed) in order to evaluate the relationship of selected SNPs and histological characteristics, meat quality and carcasses traits. Results: Mapping of detected genetic variants to QTL regions showed that chromosome 14 was the most overrepresented with the identification of four QTLs related to percentage of fiber types I and IIA. The association study performed on a 293 longissimus muscle samples confirmed a significant positive effect of transforming acidic coiled-coil-containing protein 2 (TACC2) polymorphisms on fiber diameter, while SNP within forkhead box O1 (FOXO1) locus was associated with decrease of diameter of fiber types IIA and IIB. Moreover, subsequent general linear model analysis showed significant relationship of FOXO1, delta 4-desaturase, sphingolipid 1 (DEGS1), and troponin T2 (TNNT2) genes with loin 'eye' area, FOXO1 with loin weight, as well as FOXO1 and TACC2 with lean meat percentage. Furthermore, the intramuscular fat content was positively associated (p<0.01) with occurrence of polymorphisms within DEGS1, TNNT2 genes and negatively with occurrence of TACC2 polymorphism. Conclusion: This study's results indicate that the SNP calling analysis based on RNA-seq data can be used to search candidate genes and establish the genetic basis of phenotypic traits. The presented results can be used for future studies evaluating the use of selected SNPs as genetic markers related to muscle histological profile and production traits in pig breeding.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.4
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• pp.473-479
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• 2018

Objective: The study was designed to perform a genome-wide association (GWA) and partitioning of genome using Illumina's PorcineSNP60 Beadchip in order to identify variants and determine the explained heritability for the total number of teats in Yorkshire pig. Methods: After screening with the following criteria: minor allele frequency, $MAF{\leq}0.01$; Hardy-Weinberg equilibrium, $HWE{\leq}0.000001$, a pair-wise genomic relationship matrix was produced using 42,953 single nucleotide polymorphisms (SNPs). A genome-wide mixed linear model-based association analysis (MLMA) was conducted. And for estimating the explained heritability with genome- or chromosome-wide SNPs the genetic relatedness estimation through maximum likelihood approach was used in our study. Results: The MLMA analysis and false discovery rate p-values identified three significant SNPs on two different chromosomes (rs81476910 and rs81405825 on SSC8; rs81332615 on SSC13) for total number of teats. Besides, we estimated that 30% of variance could be explained by all of the common SNPs on the autosomal chromosomes for the trait. The maximum amount of heritability obtained by partitioning the genome were $0.22{\pm}0.05$, $0.16{\pm}0.05$, $0.10{\pm}0.03$ and $0.08{\pm}0.03$ on SSC7, SSC13, SSC1, and SSC8, respectively. Of them, SSC7 explained the amount of estimated heritability along with a SNP (rs80805264) identified by genome-wide association studies at the empirical p value significance level of 2.35E-05 in our study. Interestingly, rs80805264 was found in a nearby quantitative trait loci (QTL) on SSC7 for the teat number trait as identified in a recent study. Moreover, all other significant SNPs were found within and/or close to some QTLs related to ovary weight, total number of born alive and age at puberty in pigs. Conclusion: The SNPs we identified unquestionably represent some of the important QTL regions as well as genes of interest in the genome for various physiological functions responsible for reproduction in pigs.

• BMB Reports
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• v.43 no.3
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• pp.212-218
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• 2010

Zinc finger-containing transcription factors are the largest single family of transcriptional regulators in mammals, which play an essential role in cell differentiation, cell proliferation, apoptosis, and neoplastic transformation. Here we have cloned a novel KRAB-related zinc finger gene, ZNF424, encoding a protein of 555aa. ZNF424 gene consisted of 4 exons and 3 introns, and mapped to chromosome 19p13.3. ZNF424 gene was ubiquitously expressed in human embryo tissues by Northern blot analysis. ZNF424 is conserved across species in evolution. Using a GFP-labeled ZNF424 protein, we demonstrate that ZNF424 localizes mostly in the nucleus. Transcriptional activity assays shows ZNF424 suppresses transcriptional activity of L8G5-luciferase. Overexpression of ZNF424 in HEK-293 cells inhibited the transcriptional activity of NFAT and p21, which may be silenced by siRNA. The results suggest that ZNF424 protein may act as a transcriptional repressor that suppresses NFAT and p21 pathway to mediate cellular functions.

• Journal of Microbiology and Biotechnology
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• v.22 no.4
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• pp.555-562
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• 2012

PCR was performed to analyze the ${\beta}$-lactamase genes carried by ampicillin-resistant Vibrio spp. strains isolated from marine environments in Korea between 2006 and 2009. All 36 strains tested showed negative results in PCR with the primers designed from the nucleotide sequences of various known ${\beta}$-lactamase genes. This prompted us to screen new ${\beta}$-lactamase genes. A novel ${\beta}$-lactamase gene was cloned from Vibrio alginolyticus KV3 isolated from the aquaculture water of Geoje Island of Korea. The determined nucleotide sequence (VAK-3 ${\beta}$-lactamase) revealed an open reading frame (ORF) of 852 bp, encoding a protein of 283 amino acids (aa), which displayed low homology to any other ${\beta}$-lactamase genes reported in public databases. The deduced 283 aa sequence of VAK-3, consisting of a 19 aa signal peptide and a 264 aa mature protein, contained highly conserved peptide segments specific to class A ${\beta}$-lactamases including the specific amino acid residues STFK (62-65), SDN (122-124), E (158), and RTG (226-228). Results from PCR performed with primers specific to the VAK-3 ${\beta}$-lactamase gene identified 3 of the 36 isolated strains as V. alginolyticus, Vibrio cholerae, and Photobacterium damselae subsp. damselae, indicating the utilization of various ${\beta}$-lactamase genes including unidentified ones in ampicillin-resistant Vibrio spp. strains from the marine environment. In a mating experiment, none of the isolates transfered the VAK-3 ${\beta}$-lactamase gene to the Escherichia coli recipient. This lack of mobility, and the presence of a chromosomal acyl-CoA flanking sequence upstream of the VAK-3 ${\beta}$-lactamase gene, led to the assumption that the location of this new ${\beta}$-lactamase gene was in the chromosome, rather than the mobile plasmid. Antibiotic susceptibility of VAK-3 ${\beta}$-lactamase was indicated by elevated levels of resistance to penicillins, but not to cephalosporins in the wild type and E. coli harboring recombinant plasmid pKV-3, compared with those of the host strain alone. Phylogenetic analysis showed that VAK-3 ${\beta}$-lactamase is a new and separate member of class A ${\beta}$-lactamases.

• Korean Journal of Animal Reproduction
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• v.26 no.1
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• pp.33-39
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• 2002

This study was conducted to investigate the effect of $Ca^{2+}$ concentration in fusion medium on the fusion, nuclear morphology and the development of bovine somatic cell nuclear transfer embryos. Bovine skin cells were transferred into an enucleated oocyte and fused with cytoplasm in the fusion medium containing with 0.05 to 1.0 mM Cacl$_2$. Nuclear transfer embryos were activated with a combination of A23187 and cycloheximide. Nuclear transfer embryos were fixed at 3 h after fusion or cultured for 7 ~8 days. Fusion rate was significantly (P＜0.01) increased by increasing the $Ca^{2+}$ concentrations in the fusion medium from 0.05 mM (56.6%) to 0.5 mM (50.1%) and 1.0 mM (84.3%). More than 80% of reconstituted embryos underwent premature chromosome condensation (PCC) with 0.05, 0.1 mM CaCl$_2$, whereas 54.5% and 59.3% of embryos formed pronucleus (PN) directly without PCC in the 0.5 and 1.0 mM CaCl$_2$, groups. Blastocyst formation rates were significantly (P＜0.05) different between 0.1 mM and 1.0 mM CaCl$_2$groups. From the present result, it is suggested that the elevated $Ca^{2+}$ concentrations in fusion medium can enhance the fusion and blastocyst formation rates of bovine nuclear transfer embryos.bryos.

• Journal of Life Science
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• v.18 no.6
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• pp.770-775
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• 2008

Several studies reported quantitative trait loci (QTL) for meat quality on porcine chromosome 2. For application of the chromosomal information to pig industry through using DNA technology, single nucleotide polymorphism (SNP) markers are developed by comparative re-sequencing of polymerase chain reaction (PCR) products of 13 candidate genes. A total of 34 SNPs were identified in 11 PCR products, an average of one SNP in every 296 bp.PCR restriction fragment length polymorphism (RFLP) assays were developed for 11 SNPs and used to genotype four commercial pig populations in Korea. The SNP markers were used to map candidate genes in QTL and to clarify the relevance of SNP and quantitative traits.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.14 no.2
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• pp.195-199
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• 2014

The X-linked adrenoleukodystrophy (X-ALD) is a peroxisomal disease by defects of ABCD1 gene on chromosome Xq28 leading to accumulation of saturated very long chain fatty acids (VLCFA), progressive demyelination and adrenal insufficiency. A 4-year-old boy was visited hospital with the chief compliant of hyperpigmentation beginning at 2-years old. Serum adrenocorticotropic hormone (ACTH) and cortisol concentration were compatible with adrenal insufficiency. The elevated plasmatic concentration of VLCFA and genotype analysis with sequencing of ABCD1 gene established the diagnosis of X-ALD. Brain MRI showed no abnormal high signal intensity on the white matter. Steroid replacement was started with good response. He initiated Lorenzo's oil with restriction of VLCFA by reducing the intake of fatty foods. The author highlight the importance of suspecting of X-ALD in the etiology of primary adrenal insufficiency as the first sign of the disease.

• Korean Journal of Microbiology
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• v.40 no.4
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• pp.348-354
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• 2004

The expression and antibacterial. activity of recombinant human lactoferrin (hLf) was studied from meth­ylotrophic yeast Pichia pastoris. The gene encoding hLf, isolated from human breast cDNA library, was subcloned into the expression vector, pPIC3.5K under the control of AOX1 promoter. The gene was integrated into the host chromosome and was identified by Southern blotting. The expression of the integrated gene was investigated by RT-PCR, Northern blotting, SDS-PAGE and Western blotting. Discrete band corresponding to hLf was detected from the SDS-PAGE, which was confirmed by Western blotting. The expression was also confirmed by RT-PCR and Northern blotting. The antibacterial activity of the recombinant hLf (rhLf) was investigated using Staphy­lococcus aureus ATCC 6538P and Micrococcus flavus ATCC 10240 as test organisms. The rhLf showed strong antibacterial activities against the bacteria. Furthermore, many Gram-negative animal pathogens such as E.coli ATCC8739, 25922, and Salmonella typhimurium 114 and 115, Pseudomonas fluorescens ID 963 I, P. aeruginosa KCCM 11802, and Gram-positive bacteria Bacillus mesentericus were also inhibited in their growth by the rhLf.

• Journal of Crop Science and Biotechnology
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• v.10 no.4
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• pp.265-276
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• 2007

The 13 major blast resistance(R) genes against Magnaporthe grisea were screened in a number of Korean rice varieties using molecular markers. Of the 98 rice varieties tested, 28 were found to contain the Pia gene originating from Japanese japonica rice genotypes. The Pib gene from BL1 and BL7 was incorporated into 39 Korean japonica varieties, whereas this same gene from the IRRI-bred indica varieties was detected in all Tongil-type varieties. We also found that 17 of the japonica varieties contained the Pii gene. The Pii gene in Korean rice varieties originates from the Korean japonica variety Nongbaeg, and Japanese japonica varieties Hitomebore, Inabawase, and Todorokiwase. The Pi5 gene, which clusters with Pii on chromosome 9, was identified only in Taebaeg. Thirty-four varieties were found to contain alleles of the resistance gene Pita or Pita-2. The Pita gene in japonica varieties was found to be inherited from the Japanese japonica genotype Shimokita, and the Pita-2 gene was from Fuji280 and Sadominori. Seventeen japonica and one Tongil-type varieties contained the Piz gene, which in the japonica varieties originates from Fukuhikari and 54BC-68. The Piz-t gene contained in three Tongil-type varieties was derived from IRRI-bred indica rice varieties. The Pi9(t) gene locus that is present in Korean japonica and Tongil-type varieties was not inherited from the original Pi9 gene from wild rice Oryza minuta. The Pik-multiple allele genes Pik, Pik-m, and Pik-p were identified in 24 of the varieties tested. In addition, the Pit gene inherited from the indica rice K59 strain was not found in any of the Korean japonica or Tongil-type varieties tested.