• Journal of Animal Science and Technology
• /
• v.53 no.1
• /
• pp.15-22
• /
• 2011

The purpose of this study was to analyse of association between growth traits and single nucleotide polymorphisms (SNPs) polymorphism of phosphoglycerate kinase 2 (PGK 2) gene in pigs. The birth weight of piglet influences on weaning weight and survival rate that are import economic traits in pig industry. Also, these growth traits are representative factor to decrease a period getting to marketing weight as well as growth rate in pig. The PGK 2 is an isozyme that catalyzes the first ATP-generating step in the glycolytic pathwayand important enzyme related with energy metabolism. Twenty of SNPs were discoveredby genome structure analysis that compares the sequence on promoter and transcription region of PGK 2 gene in porcine chromosome 7. An association between PGK 2 SNPs and growth traits was analyzed in $F_2$ reciprocal-crossbred population between korean native pig (KNP) and Landrace. Association analysis indicated that polymorphism of the PGK 2 gene promoter region has significant effects on weight at birth (p<0.01) and weight at 3 weeks of age (p<0.0001). These results suggest that PGK 2 gene polymorphism was associated with energy metabolism and physiological function of growth in pig.

• Asian-Australasian Journal of Animal Sciences
• /
• v.33 no.10
• /
• pp.1558-1565
• /
• 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 Life Science
• /
• v.26 no.1
• /
• pp.1-7
• /
• 2016

Fatness is one of the most important economic traits in pigs. The leptin receptor (LEPR) gene may be a potential candidate for the fatness quantitative trait locus (QTL) on porcine chromosome 6, due to its position and physiological role. Thus, this study was carried out to evaluate the associations between structural variants in the LEPR gene and economic traits in pigs. We obtained an approximately 114-kb sequence containing the complete genomic DNA of the porcine LEPR gene, using shotgun sequencing of a bacterial artificial chromosome clone. We report the complete genomic structure of the porcine LEPR gene. Dozens of transcription factor-binding sites were found in the 1.2 kb upstream region from the transcription start point. An association study was performed with 550 Duroc pigs for 24 single-nucleotide polymorphisms (SNPs), including 6 SNPs within exons and 18 SNPs within the putative 5‘ regulatory region of the porcine LEPR gene. Among them, one SNP (−790C/G) was significantly associated with backfat thickness and lean meat percentage, whereas the others, including two SNPs with missense polymorphisms, had no effect on any phenotype. These results suggest that SNP −790C/G may be a useful marker for genetic improvements of fatness and leanness in Duroc pigs.

• Korean Journal of Plant Taxonomy
• /
• v.34 no.4
• /
• pp.335-358
• /
• 2004

To investigate molecular phylogenetic relationships and to test hypothesis of hybrid origin of Ranunculus cantoniensis (Ranunculaceae), the sequences of nrDNA and chloroplast DNA were analyzed for 8 taxa and 25 accessions including 5 accessions of outgroup. In the phylogenetic trees by analyses of maximum parsimony and maximum likelihood for ITS nrDNA sequences and combined data of psbA-trnH, rps16 and trnL sequences of cpDNA, R. cantoniensis was most closely related to R. chinensis, and then to R. taciroi and R. silerifolius. The molecular phylogenetic relationships were not congruent with the previous report that R. cantoniensis was most closely related to R. silerifolius. In the sequence analysis of ITS and psbA-trnH, rps16, trnL for R. cantoniensis and the related taxa, R. cantoniensis showed polymorphism. It supported that the polymorphism also was reported in chromosome number and karyotype of R. cantoniensis. Ranunculus cantoniensis shared the marker gene of R. chinensis and R. silerifolius in ITS, and one of R. silerifolius in cpDNA. These results supported the hypothesis that R. cantoniensis was caused by hybridization between R. chinensis and R. silerifolius based on chromosome number and karyotype, and also estimated that R. silerifolius might be of maternal origin and R. chinensis be paternal.

• Journal of Genetic Medicine
• /
• v.2 no.1
• /
• pp.41-47
• /
• 1998

Human uniparental gestations such as gynogenetic ovarian teratomas provide a model to evaluate the integrity of parent-specific gene expression - i.e. imprinting - in the absence of a complementary parental genetic contribution. The few imprinted genes characterized so far include the insulin-like growth factor-2 gene (IGF2) coding for a fetal growth factor and H19 gene whose normal function is unknown but it is likely to act as an mRNA. IGF2 is expressed by the paternal allele and H19 by the maternal allele. This reciprocal expression is quite interesting because both H19 and IGF2 genes are located close to each other on chromosome 11p15.5. In situ RNA hybridization analysis has shown variable expression of the H19 and IGF2 alleles according to the tissue origin in 11 teratomas. Especially, Skin, derivative of ectoderm, is expressed conspicuously. We examined imprinting of H19 and IGF2 in teratomas using PCR and RT-PCR of exonic polymorphism. H19 and IGF2 transcript could be expressed either biallelically or monoallelically in the teratomas. Biallelic expression (i.e., loss of imprinting) of IGF2 occurred in 5 out of 6 mature teratomas and 1 out of 1 immature teratoma. Biallelic expression of H19 occurred in 4 out of 10 mature teratomas and 1 out of 1 immature teratoma. Expression levels of H19 and IGF2 transcript using the semi-quantitative RT-PCR had no relation between monoallelic and biallelic expression. Moreover, IGF2 biallelic expression did not affect allele-specificity or levels of H19 expression. These results demonstrate that both genes, H19 and IGF2, can be imprinted, expressed and regulated independently and individually of each other in ovarian teratoma.

• Asian-Australasian Journal of Animal Sciences
• /
• v.20 no.5
• /
• pp.615-621
• /
• 2007

AMP-activated protein kinase alpha 2 (PRKAA2) plays a key role in regulation of fatty acid and cholesterol metabolism. This study investigated the porcine PRKAA2 gene as a positional candidate for intramuscular fat and backfat thickness traits in pig chromosome 6. A partial fragment of the porcine PRKAA2 gene, amplified by PCR, contained a putative intron 3 including a part of exon 3 and 4, comparable with that of human PRKAA2 gene. Within the fragment, several single nucleotide polymorphisms were identified using multiple sequence alignments. Of these, TaqI restriction enzyme polymorphism was used for genotyping various pig breeds including Korean reference family. Using linkage and physical mapping, the porcine PRKAA2 gene was mapped in the region between microsatellite markers SW1881 and SW1680 on chromosome 6. Allele frequencies were quite different among pig breeds. The full length cDNA of the porcine PRKAA2 (2,145 bp) obtained by RACE containing 1,656 bp open reading frame of deduced 552 amino acids, had sequence identities with PRKAA2 of human (98.2%), rat (97.8%), and mouse (97.5%). These results suggested that the porcine PRKAA2 is a positional candidate gene for fat deposition trait at near telomeric region of the long arm of SSC 6.

• Clinical and Experimental Reproductive Medicine
• /
• v.42 no.2
• /
• pp.58-61
• /
• 2015

Objective: The XIST gene is considered to be an attractive candidate gene for skewed X-chromosome inactivation and a possible cause of primary ovarian insufficiency (POI). The purpose of this study was to investigate whether the XIST gene promoter mutation is associated with idiopathic POI in a sample of the Korean population. Methods: Subjects consisted of 102 idiopathic POI patients and 113 healthy controls with normal menstrual cycles. Patients with the following known causes of POI were excluded in advance: cytogenetic abnormalities, prior chemo- or radiotherapy, or prior bilateral oophorectomy. Genotyping was performed using polymerase chain reaction-restriction fragment length polymorphism analysis. Results: The mean age of onset of ovarian insufficiency was $28.7{\pm}8.5years$ and the mean values of serum luteinizing and follicle-stimulating hormones and estradiol in the POI group were $31.4{\pm}18.2mIU/mL$, $74.5{\pm}41.1mIU/mL$, and $30.5{\pm}36.7pg/mL$, respectively. We found no cytosine to guanine (C43G) variation in the XIST gene in both POI patients and controls. Conclusion: The C43G mutation in the promoter region of the XIST gene was not present in the Korean patients with idiopathic POI in our study, in contrast to our expectation, suggesting that the role of XIST in the pathogenesis of POI is not yet clear.

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

• Korean Journal of Medicinal Crop Science
• /
• v.3 no.1
• /
• pp.61-65
• /
• 1995

Karyotype analysis was carried out in four lines of Bupleurum falcatum L. cultivated in Korea and SDS-PAGE was applied to determine the seed protein profiles among the lines. Chromosomes were classified into two groups, large and small ones. Two kinds of karyotype, 2n=20 and 2n=26, were identified. Chromosome 1 of 2n=20 were all submedian, while that of 2n=26 were median. Chromosomes 2, 3 and 5 of 2n=20 showed polymorphism in size and arm-ratio. Chromosome 2 was submedian, while others were median in the line of 2n=26. Karyotypcs of cultivars native of Korea were similiar each other, while those introduced from Japan showed different patterns. In SDS PAGE gels, qualitative difference s in high molecular weight proteins, more than 45KD, were detected among the lines. The numbers of specific band were three in lines of 2n=20 and two in 2n=26.

• Journal of Genetic Medicine
• /
• v.18 no.2
• /
• pp.110-116
• /
• 2021

Microdeletions of chromosome 22q11.2 are one of the most common microdeletions occurring in humans, and is known to be associated with a wide range of highly variable features. These deletions occur within a cluster of low copy repeats (LCRs) in 22q11.2, referred to as LCR22 A-H. DiGeorge (DGS)/velocardiofacial syndrome is the most prevalent form of a 22q11.2 deletions, caused by mainly proximal deletions between LCR22 A and D. As deletions of distal portion to the DGS deleted regions has been extensively studied, the recurrent distal 22q11.2 microdeletions distinct from DGS has been suggested as several clinical entities according to the various in size and position of the deletions on LCRs. We report a case of long-term follow-up of a female diagnosed with a 22q11.2 distal deletion syndrome, identified a deletion of 1.9 Mb at 22q11.21q11.23 (chr22: 21,798,906-23,653,963) using single nucleotide polymorphism array. This region was categorized as distal deletion type of 22q11.2, involving LCR22 D-F. She was born as a preterm, low birth weight to healthy non-consanguineous Korean parents. She showed developmental delay, growth retardation, dysmorphic facial features, and mild skeletal deformities. The patient underwent a growth hormone administration due to growth impairment without catch-up growth. While a height gain was noted, she had become overweight and was subsequently diagnosed with pre-diabetes. Our case could help broaden the genetic and clinical spectrum of 22q11.2 distal deletions.