• Animal cells and systems
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• v.1 no.1
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• pp.123-128
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• 1997

The characteristics of allelic polymorphisms of the two (CA)n microsatellite (p599 and ㅅ599) markers spanning the long arm of chromosome 5 were studied in 52 DNA samples from unrelated inhabitants of Seoul (Korea) by using the polymerase chain reaction (PCR) to investigate differences in allele frequencies between Korean and Caucasian populations. The 6 alleles were observed for p599 (CA)n with a polymorphism informative content (PIC) value of 0.71 and 9 alleles for ㅅ599 (CA)n with a PIC value of 0.82. The observed heterozygote frequencies of the loci were estimated to 0.730 and 0.846, respectively. Several allele frequencies of two loci showed significant differences between Korean and Caucasian populations. Genotype data from the two loci were consistent with the Hardy-Weinberg equilibrium by x2 test. Linkage disequilibrium between p599 (CA)n and ㅅ599 (CA)n loci was observed in x2 test between the observed and expected frequency of allelic association. The probability of matching calculated at each locus was 0.104 for p599 (CA)n and 0.043 for ㅅ599 (CA)n, respectively. These results demonstrate the need to determine populationspecific allele frequency distributions for polymorphic markers when performing genetic linkage studies in racially defined several populations.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.7
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• pp.926-935
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• 2015

The efficiency of genome-wide association analysis (GWAS) depends on power of detection for quantitative trait loci (QTL) and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage disequilibrium single locus regression method (LDRM), a combined linkage and linkage disequilibrium analysis (LDLA) and a $BayesC{\pi}$ approach. The phenotypes of 486 steers were collected for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area, and marbling score (Marb). Also the genotype data for the steers and their sires were scored with the Illumina bovine 50K single nucleotide polymorphism (SNP) chips. For the two former GWAS methods, threshold values were set at false discovery rate <0.01 on a chromosome-wide level, while a cut-off threshold value was set in the latter model, such that the top five windows, each of which comprised 10 adjacent SNPs, were chosen with significant variation for the phenotype. Four major additive QTL from these three methods had high concordance found in 64.1 to 64.9Mb for Bos taurus autosome (BTA) 7 for WWT, 24.3 to 25.4Mb for BTA14 for CWT, 0.5 to 1.5Mb for BTA6 for BFT and 26.3 to 33.4Mb for BTA29 for BFT. Several candidate genes (i.e. glutamate receptor, ionotropic, ampa 1 [GRIA1], family with sequence similarity 110, member B [FAM110B], and thymocyte selection-associated high mobility group box [TOX]) may be identified close to these QTL. Our result suggests that the use of different linkage disequilibrium mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.7
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• pp.941-946
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• 2008

Single-minded 1 gene (SIM1) is a homolog of Drosophila SIM1 gene which plays a key role in the midline cell lineage of the central nervous system and is implicated in the regulation of feeding behavior and obesity in the human and mouse. In this study, porcine SIM1 gene was firstly mapped to chromosome 1p13 using radiation hybrid (RH) mapping and two polymorphisms were detected at position 607 (A/G) in SIM1 intron7 and position 780 (C/T) in SIM1 exon8. The last substitution was genotyped in a 364 F2 animal-population and an association analysis of these genotypes was performed with growth, carcass and meat quality traits by the statistical animal model. The results showed the significant influence of the SIM1 genotype on growth (p<0.05): live weight at birth, later period of growth and average daily gain; and effects on carcass composition (p<0.05): weight of head and buck kneed foreleg, backfat depth, loin eye area, carcass leaf fat and ham fat weights; and traits related to intramuscular fat content (p<0.05).

• Korean Journal of Ichthyology
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• v.28 no.4
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• pp.215-222
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• 2016

Triploidy was induced in the marine medaka, Oryzias dancena by cold shock treatment ($0^{\circ}C$) of fertilized eggs for 30, 45, or 60 min, applied two minutes after fertilization. The triploid genotype was induced by each of the thermal shock regimes tested. The best result was obtained when the eggs were treated for 45 min, which induced triploidy in all the resulting fish. Triploidy was confirmed using chromosomal and flow cytometer analyses, and erythrocyte measurements. The surface areas and volumes of the erythrocytes of triploid fish were significantly larger than those of diploid fish, and their chromosome number (3N=72) was 1.5 times greater that for the diploids (2N=48). Based on a flow cytometer analysis, the triploid fish had approximately 1.5 times the cellular DNA content (2.40 pg/cell) of the diploid specimens (1.61 pg/cell). Data from this study provide the basis for the development of unique models for studying reproductive confinement in transgenic fish.

• Clinical and Experimental Pediatrics
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• v.60 no.12
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• pp.408-412
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• 2017

Combined oxidative phosphorylation deficiency-17 (COXPD-17) is very rare and is caused by homozygous or compound heterozygous mutations in the ELAC2 gene on chromosome 17p12. The ELAC2 gene functions as a mitochondrial tRNA processing gene, and only 4 different pathogenic mutations have been reported in ELAC2-associated mitochondrial dysfunction involving oxidative phosphorylation. Affected patients show various clinical symptoms and prognosis, depending on the genotype. We report a novel mutation in the ELAC2 gene (c.95C>G [p.Pro32Arg], het), in an infant with COXPD-17 who presented with encephalopathy including central apnea and intractable epilepsy, and growth and developmental retardation. During hospitalization, consistently elevated serum lactic acid levels were noted, indicative of mitochondrial dysfunction. The patient suddenly died of shock of unknown cause at 5 months of age. This is the first case report of COXPD-17 in Korea and was diagnosed based on clinical characteristics and genetic analysis.

• Journal of Genetic Medicine
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• v.6 no.1
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• pp.67-73
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• 2009

Purpose : In spite of the karyotype and phenotype diversity in Turner syndrome patients, there are few reports about such differences in Korea. We reviewed the data of chromosome abnormalities, clinical manifestations, and comorbidities of Turner syndrome patients in Kyungpook National University Hospital to compare them to the recent hypotheses about sex chromosome gene loci related to Turner symptoms. Materials and Methods : We identified the cytologic findings of 92 patients with Turner syndrome and the clinical findings of 62 patients among them. Results : 54.3 percent of patients had 45,X while 45.7 percent showed other karyotype combinations (45,X/46,XX, 45,X/46,XX/47,XXX, 46,X,del(Xp), 46,X,del(Xq), 45,X/46,X,del(Xq), 46,X,i(Xq), 45,X/46,X,i (Xq)). The Turner symptoms found included short neck, high arched palate, broad chest, Madelung deformity, short metacarpals, scoliosis, cubitus valgus, low hair line, webbed neck, edematous extremities, pigmented nevus, and sexual infantilism. The specific diseases associated Turner syndrome included renal abnormalities, congenital heart disease, hearing defects, diabetes mellitus, hyperlipidemia, and decreased bone density. The phenotype of the mosaicism group was milder than that of the monosomy group. In the case of 46,X,del(Xp) and 45,X/46,X,del(Xq) groups, all had skeletal abnormalities, but the 46,X,del(Xq) group had none. In the case of 46,X,del(Xp) group, all showed short statures and skeletal abnormalities, but no sexual infantilism was observed. In the case of 46,X,i(Xq) and 45,X/46,X,i(Xq) groups, they all showed delayed puberty and had primary amenorrhea. Conclusion : It is important to study karyotype-phenotype correlations in patients with Turner syndrome to obtain interesting information about the genotype-phenotype correlations related to the X chromosome.

• Food Science of Animal Resources
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• v.32 no.6
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• pp.776-782
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• 2012

Marbling (intramuscular fat) is the most economically important meat quality trait in Hanwoo (Korean cattle). The endothelial differentiation G-protein coupled receptor 1 (EDG1) gene, involved in blood vessel formation, is located within the genomic region of a quantitative trait locus (QTL) for marbling on bovine chromosome 3. Thus, the EDG1 gene can be considered as a positional and functional candidate gene for meat quality in beef cattle. This study aimed to identify single nucleotide polymorphisms (SNPs) in the EDG1 gene and to evaluate their associations with carcass traits in Hanwoo population. We have sequenced a fragment of 5'-UTR of the EDG1 gene and identified one SNP. Genotyping of the g.166A>G SNP marker was carried out using PCR-RFLP analysis in 309 Hanwoo steers in order to evaluate their association with carcass traits. The g.166A>G SNP marker showed a significant effect on the marbling score. Animals with the GG genotype had higher marbling score compared with AA and AG genotypes (p<0.05). This SNP marker also showed a significant additive effects for the marbling score (p<0.05). These results suggest that the EDG1 gene can be used as a molecular marker for DNA marker-assisted selection in order to increase the levels of the marbling score in Hanwoo.

• Journal of Genetic Medicine
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• v.4 no.2
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• pp.133-141
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• 2007

Purpose : Cri-du-Chat syndrome (CdCs) is a rare but clinically recongnizable condition with an estimated incidence of 1:50,000 live births. The clinical characteristics of the syndrome include severe psychomotor and mental retardation, microcephaly, hypertelorism, hypotonia, and slow growth. Also the size of the chromosome 5p deletion ranges were known from the region 5p13 to the terminal region. In this study, we report the spectrum of 5p deletion in Korean 20 pts. with CdCs and genotype-phenotype associations in CdCs. Methods : In order to delineate genotype-phenotype correlation, molecular cytogenetic studies including GTG banding and clinical characterization were performed on Korean 20 pts with CdCs including parents. CGH array and Fluorescence in situ hybridization (FISH) analysis were used to confirm a terminal deletion karyotype and map more precisely the location of the deletion breakpoint. Results : Molecular analysis of the spectrum of 5p deletion revealed 9 pts (45%) with a del (5)(p14), 7 pts. (35%) a del (5)(p13), 3 pts. (15%) a del (5)(p15.1) and 1 pt. (5%) a del (5)(p15.2) in 20 pts with CdCs. 4(20%)pts were identified to have additional chromosome abnormalites of deficiency and duplication involving chromosomes of 6, 8, 18, & 22. Parental study identified 3 familial case (2 paternal and 1 maternal origin) showing parents being a balanced translocation carrier. And the comparison study of the deletion break points among these 20 pts. with their phenotype has showed the varying clinical pheno-types in the CdCs critical region. Conclusion : The characterization of 5p deletion including parental study may help to delineate the genotypephenotype correlation in CdCs. Also these molecular cytogenetic analyses will be able to offer better information for accurate genetic diagnosis in CdCs and further make possible useful genetic counseling in pts. and family.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.10
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• pp.1558-1565
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• 2020

Objective: The objective of this study was to characterize the number of loci affecting growth traits and the distribution of single nucleotide polymorphism (SNP) effects on growth traits, and to understand the genetic architecture for growth traits in Hanwoo (Korean cattle) using genome-wide association study (GWAS), genomic partitioning, and hierarchical Bayesian mixture models. Methods: GWAS: A single-marker regression-based mixed model was used to test the association between SNPs and causal variants. A genotype relationship matrix was fitted as a random effect in this linear mixed model to correct the genetic structure of a sire family. Genomic restricted maximum likelihood and BayesR: A priori information included setting the fixed additive genetic variance to a pre-specified value; the first mixture component was set to zero, the second to 0.0001×σ²_g, the third 0.001×σ²_g, and the fourth to 0.01×σ²_g. BayesR fixed a priori information was not more than 1% of the genetic variance for each of the SNPs affecting the mixed distribution. Results: The GWAS revealed common genomic regions of 2 Mb on bovine chromosome 14 (BTA14) and 3 had a moderate effect that may contain causal variants for body weight at 6, 12, 18, and 24 months. This genomic region explained approximately 10% of the variance against total additive genetic variance and body weight heritability at 12, 18, and 24 months. BayesR identified the exact genomic region containing causal SNPs on BTA14, 3, and 22. However, the genetic variance explained by each chromosome or SNP was estimated to be very small compared to the total additive genetic variance. Causal SNPs for growth trait on BTA14 explained only 0.04% to 0.5% of the genetic variance Conclusion: Segregating mutations have a moderate effect on BTA14, 3, and 19; many other loci with small effects on growth traits at different ages were also identified.

• Journal of Animal Science and Technology
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• v.51 no.3
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• pp.193-200
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• 2009

The pork from black-coated pigs is famous among-consumers for better eating quality. The loci affecting black coat color was identified in pig chromosome 6 in which several genetic effects on pork quality have been reported. The melanocortin 1 receptor (MC1R) gene is a major gene which plays a key role in regulation of eumelanin (black/brown) and phaeomelanin (red/yellow). In this study, the MC1R gene polymorphism was analyzed for pig breed determination and genetic association with pork quality traits. MC1R Ala243Thr variation was analyzed to determine a specific genotype for four commercial pig breeds (Landrace, Yorkshire, Berkshire and, Duroc) and a Korean native pigs (KNP). Then we developed original KNP-specific DNA markers to determine the pork from black-coated pigs using MC1R DNA sequences. The total length of the MC1R coding sequence ranged 1451bp in KNP. KNP had the 0201 allele pertaining to $E^{D1}$ but some of the KNP had the $E^P$ allele, probably reflecting the geneticintrogression of $E^P$ allele into KNP. Furthermore, a relationship between Leu102Pro single nucleotide polymorphism (SNP) genotype and pork quality phenotype were analyzed in F2 reciprocal-crossbred population between KNP and Yorkshire. Association analysis indicated that the allele of the MC1R gene has no effect on pork quality. These results suggest that black coat-color is not directly associated with preferred pork quality, but the black-coat color pig breed may have other genetic components for superior pork quality.