• Journal of Embryo Transfer
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• v.31 no.4
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• pp.313-318
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• 2016

The aim of this study was to identify quantitative trait loci (QTLs) influencing teat number traits in an $F_2$ intercross between Landrace and Korean native pigs (KNP). Three teat number traits (left;right;and total) were measured in 1105 $F_2$ progeny. All experimental animals were genotyped with 173 informative microsatellite markers located throughout the pig genome. We detect that seven chromosomes harbored QTLs for teat number traits: genome regions on SSC1;3;7;8;10;11;and 13. Six of fourteen identified QTL reached genome-wide significance. In SSC7;we identified a major QTL affecting total teat number that accounted for 5.6 % of the phenotypic variance;which was the highest test statistic (F-ratio = 61.1 under the additive model;nominal $P=1.3{\times}10^{-14}$) observed in this study. In this region;QTL for left and right teat number were also detected with genome-wide significance. With exception of the QTL in SSC10;the allele from KNP in all 6 identified QTLs was associated with decreased phenotypic values. In conclusion;our study identified both previously reported and novel QTL affecting teat number traits. These results can play an important role in determining the genetic structure underlying the variation of teat number in pigs.

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

• Journal of Korean Neurosurgical Society
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• v.48 no.1
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• pp.14-19
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• 2010

Objective : Allelic losses or loss of heterozygosity (LOH) at many chromosomal loci have been found in the cells of meningiomas. The objective of this study was to evaluate LOH at several loci of different chromosomes (1p32, 17p13, 7q21, 7q31, and 22q13) in different grades of meningiomas. Methods : Forty surgical specimens were obtained and classified as benign, atypical, and anaplastic meningiomas. After DNA extraction, ten polymorphic microsatellite markers were used to detect LOH. Medical and surgical records, as well as pathologic findings, were reviewed retrospectively. Results : LOH at 1p32 was detected in 24%, 60%, and 60% in benign, atypical, and anaplastic meningiomas, respectively. Whereas LOH at 7q21 was found in only one atypical meningioma. LOH at 7q31 was found in one benign meningioma and one atypical meningioma. LOH at 17p13 was detected in 4%, 40%, and 80% in benign, atypical, and anaplastic meningiomas, respectively. LOH at 22q13 was seen in 48%, 60%, and 60% in benign, atypical, and anaplastic meningiomas, respectively. LOH results at 1p32 and 17p13 showed statistically significant differences between benign and non-benign meningiomas. Conclusion : LOH at 1p32 and 17p13 showed a strong correlation with tumor progression. On the other hand, LOH at 7q21 and 7q31 may not contribute to the development of the meningiomas.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2018.10a
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• pp.25-25
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• 2018

The Fukushima Daiichi Nuclear Power Plant accident in March 2011 caused severe radioactive contamination in the surrounding environment. Since the accident, much attention has been paid to the biological and genetic consequences of organism inhabiting the contaminated area. The effect of radiation exposure on genetic mutation rates is little known, especially for low doses and in situ conditions. Evaluating DNA mutation by low levels of radiation dose is difficult due to the rare mutation event and lack of sequence information before the accident. In this study, correlations with air dose levels and somatic DNA mutation rates were evaluated using Next Generation Sequencer for the clonal plant, Phyllostachys edulis. This bamboo is known to spread an identical clone throughout Japan, and it has the advantage that we can compare genetic mutation rate among identical clone growing different air dose levels. We collected 94 samples of P. edulis from 14 sites with air dose rates from $0.04{\sim}7.80{\mu}Gy/h$. Their clonal identity was confirmed by analysis using 24 microsatellite markers, and then, sequences among samples were compared by MIG sequence. The sequence data were obtained from 2,718 loci. About ~200,000 bp sequence (80 bp X 2,718 loci) were obtained for each sample, and this corresponds to about 0.01% of the genome sequence of P. edulis. In these sequences, 442 loci showed polymorphism patterns including recent origin mutation, old mutation, and sequence errors. The number of mutations per sample ranged from 0 to 13, and did not correlate with air dose levels. This result indicated that DNA mutations have not accumulated in P. edulis living in the air doses levels less than $10{\mu}Gy/h$. Our study also suggests that mutation rates can be assessed by selecting an appropriate experimental approach and analyzing with next generation sequencer.

• Genomics & Informatics
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• v.1 no.2
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• pp.101-107
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• 2003

Loss of heterozygosity (LOH) has been used to detect deleted regions of a specific chromosome in cancer cells. LOH on chromosome 16q has been reported to occur frequently in progressed hepatocellular carcinoma (HCC). Liver tissues from 37 Korean HCC patients were analyzed for LOH by using 25 polymorphic microsatellite markers distributed along 16q. Out of the 37 HCC patients studied, 21 patients (56.8%) showed LOH in various regions of 16q with at least one polymorphic marker. Puring the analysis of these 21 LOH cases, 6 patients showed interstitial LOHs in which the boundary of the LOH region was defined. With two rounds of LOH analysis, five commonly occurring interstitial LOH regions were identified; 16q21-22.1, 16q22.2 - 22.3, 16q22.3, 16q23.2 and 16q23.3 - 24.1. Among the five LOH regions the 16q23.3 - 24.1 region has been reported to be related with chromosome instability. A complete physical map, which covers the 3.2 Mb region of 16q23.3 - 24.1 (D16S402 and D16S486), was constructed to identify novel candidate tumor suppressor genes. We provide the minimally tiling path map consisting of 28 BAC clones. There was one gap between NT_10422.11 and NT_019609.9 of the human genome sequence contig (NCBI sequence build 33, April 29, 2003). This gap can be filled by sequencing the R-1425M20 clone which bridges these sequence contigs.

• Journal of Genetic Medicine
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• v.1 no.1
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• pp.33-37
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• 1997

Spinal muscular atrophy (SMA) is the second most common fatal disease of childhood with autosomal dominant mode of inheritance, and in its less severe form the third most common neuromuscular disease of childhood after Duchenne muscular dystrophy. The genetic defect was found to be on the long arm of chromosome 5 (5q11.2-q13.3) where many genes and microsatellite markers were missing. One of the most important genes is the Survival Motor Neuron (SMN) gene which is homozygously missing in 90% of SMA patients. Another important gene, the Neuronal Apoptosis Inhibitory Protein (NAIP) gene was found to be defective in 67% of SMA type I patients. Studies so far suggest SMA occurs when the genes on the long arm of chromosome 5 are mutated or deleted. Recently our hospital encountered 2 SMA patients of type I and II respectively. These patients both had homozygously defective SMN genes but intact NAIP genes. We are reporting these cases with bibliographic review and discussion. Korean SMA patients presumably have defects in SMN genes similar to those found in European patients, although the significance of NAIP genes remains to be established. SMN gene defects can be easily diagnosed using PCR and restriction enzymes, and this method could be applied towards convenient prenatal diagnosis and towards screening for family members at risk.

• Korean Journal of Head & Neck Oncology
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• v.20 no.2
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• pp.147-155
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• 2004

Objectives: Head and neck squamous cell carcinoma (HNSCC) is the most common head and neck malignant tumor. The molecular genetic changes involving both oncogenes and tumor suppressor genes are known to be involved in head and neck squamous cell carcinogenesis, but the roles of the known tumor suppressor genes in carcinogenesis are not fully elucidated. The objectives of this study are to demonstrate the genetic alterations including the loss of heterozygosity (LOH) , amplification, and microsatellite instability of known tumor suppressor genes in HNSCC and to evaluate the relationship between genetic alterations of tumor suppressor genes and clinicopathologic features. Materials and Methods: Genetic alterations of 10 micro satellite markers of the 6 known tumor suppressor genes (APC, EXT1, DPC4, p16, FHIT, and PTEN) were analysed by DNA-PCR in paraffin-embedded histologically confirmed HNSCC specimens. Results: The genetic alterations of tumor suppressor genes were found frequently. Among the genetic alterations, LOH was most frequently found one. LOH was found frequently in APC (45.4%), EXT1 (36.4%), DPC4 (54.5%), and p16 (50%), but not found in FHIT. Also, the author found that abnormalities of APC gene was related to cervical lymph node metastasis and recurrence and that abnormalities of EXT1 gene were coexisted with those of APC gene or DPC4 gene. But these coexistences had no correlation with clinical features. Conclusion: These results suggested that APC, EXT1, p16, and DPC4 genes might play important roles and multiple tumor suppressor genes may participate dependently or independently in the carcinogenesis of HNSCC. These results also suggested that APC gene might relate to prognosis.

• Genomics & Informatics
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• v.6 no.1
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• pp.8-13
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• 2008

High-density lipoprotein (HDL) whose primary role is to transport cholesterol from peripheral tissues to the liver, is associated with the incidence of coronary heart disease. We analyzed HDL cholesterol levels in a genetically isolated population of extended Mongolian families. A total of 1002 individuals (54.5% women) from 95 families were enrolled. After genotyping by use of 1000 microsatellite markers, we performed a genome-wide linkage search with variance component analysis. The estimated heritability of HDL cholesterol was 0.45, revealing that HDL cholesterol was under significant genetic influence. We found peak evidence of linkage (LOD score=1.88) for HDL cholesterol level on chromosome 6 (nearest marker D6S1660) and potential evidences for linkage on chromosomes 1, 12 and 19 with the LOD scores of 1.32, 1.44 and 1.14, respectively. These results should pave the way for the discovery of the relevant genes by fine mapping and association analysis.

• The Plant Pathology Journal
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• v.19 no.1
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• pp.24-29
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• 2003

SS2-2, a hypernodulating soybean mutant was isolated by EMS mutagenesis from Sinpaldalkong 2. This auto-regulation mutant showed greater number of nodules and smaller plant size than its wild type Sinpaldalkong 2. SSR markers were used to identify DNA variation at SSR loci from different soybean LG. The only SSR marker that detected a length polymorphism between SS2-2 and its wild type ancestor was Satt294 on LG C1 instead of LG H, locating a hypernodulating gene. Sequencing data of flanking Satt294 indicated that the size variation was due to extra stretch of TTA repeats of the SSR motif in SS2-2, along with $A\longrightarrow$G transversion. In spite of phenotypic differences between the wild type and its hypernodulating mutants, genomic DNA poly-morphisms at microsatellite loci could not control regulation of nodule formation. The cDNA-AFLP method was applied to compare differential display of cDNA between Sinpaldalkong 2 and SS2-2. After isolation and sequence comparison with many AELP fragments, several interesting genes were identified. Northern blot analysis, immunolocalization and/or the yeast two-hybrid system with these genes might provide information on regulation of nodule development in SS2-2.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.65 no.1
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• pp.1-21
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• 2020

Association mapping is widely used in rice and other crops to identify genes underlying important agronomic traits. Most association mapping studies use diversity panels comprising accessions with various geographical origins to exploit their wide genetic variation. While locally adapted breeding lines are rarely used in association mapping owing to limited genetic diversity, genes/alleles identified from elite germplasm are practically valuable as they can be directly utilized in breeding programs. In this study, we analyzed genetic diversity of 179 rice varieties (161 japonica and 18 Tongil-type) released in Korea from 1970 to 2006 using 192 microsatellite markers evenly distributed across the genome. The 161 japonica rice varieties were genetically very close to each other with limited diversity as they were developed mainly through elite-by-elite crosses to meet the specific local demands for high quality japonica rice in Korea. Despite the narrow genetic background, abundant phenotypic variation was observed in heading time, culm length, and amylose and protein content in the 161 japonica rice varieties. Using these varieties in association mapping, we identified six, seven, ten, and four loci significantly associated with heading time, culm length, and amylose and protein content, respectively. The sums of allelic effects of these loci showed highly significant positive correlation with the observed phenotypic values for each trait, indicating that the allelic variation at these loci can be useful when designing cross combinations and predicting progeny performance in local breeding programs.