• Journal of Life Science
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• v.22 no.3
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• pp.366-372
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• 2012

This study was conducted to estimate the extent of linkage disequilibrium (LD) and effective population size using whole genomic single nucleotide polymorphisms (SNP) genotyped by DNA chip in Hanwoo. Using the blood samples of 35 young bulls born from 2005 to 2008 and their progenies (N=253) in a Hanwoo nucleus population collected from Hanwoo Improvement Center, 51,582 SNPs were genotyped using Bovine SNP50 chips. A total of 40,851 SNPs were used in this study after elimination of SNPs with a missing genotyping rate of over 10 percent and monomorphic SNPs (10,730 SNPs). The total autosomal genome length, measured as the sum of the longest syntenic pairs of SNPs by chromosome, was 2,541.6 Mb (Mega base pairs). The average distances of all adjacent pairs by each BTA ranged from 0.55 to 0.74 cM. Decay of LD showed an exponential trend with physical distance. The means of LD ($r^2$) among syntenic SNP pairs were 0.136 at a range of 0-0.1 Mb in physical distance and 0.06 at a range of 0.1-0.2 Mb. When these results were used for Luo's formula, about 2,000 phenotypic records were found to be required to achieve power > 0.9 to detect 5% QTL in the population of Hanwoo. As a result of estimating effective population size by generation in Hanwoo, the estimated effective population size for the current status was 84 heads and the estimate of effective population size for 50 generations of ancestors was 1,150 heads. The average decreasing rates of effective population size by generation were 9.0% at about five generations and 17.3% at the current generation. The main cause of the rapid decrease in effective population size was considered to be the intensive use of a few prominent sires since the application of artificial insemination technology in Korea. To increase and/or sustain the effective population size, the selection of various proven bulls and mating systems that consider genetic diversity are needed.

• Korean Journal of Microbiology
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• v.26 no.4
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• pp.283-290
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• 1988

A spontaneous revertant of mutation rbsB103 that is ribose taxis-positive was characterized. This revertant was found to be export-competent in the export of ribose-binding protein shown by the disappearance of accumulated mutant precursor protein and the export of mature ribose-binding protein to the periplasm. The reversional change was shown to be in the region of risB gene that codes for the amino terminal portion of ribose-binding protein. Analysis by high-performance liquid chromatography of peptide patterns of ribose-binding proteins confirmed the relationship between the wild-type and the revertant proteins as shown for the mutant previously (Iida et al., 1985). When the processing rate of presursor proteins from the wild type and the revertant strain in vivo was compared by pulse-chase experiment, it was found that processing is less efficient than normal in the revertant. Purified mature proteins from both wild-type and revertant were subjected to amino acid sequencing. The results confirmed the amino acid changes deduced from the DNA sequencing and showed that processing of the revertant precursor occured in the correct position even though there are two different amino acids present in the signal sequence.

• Korean Journal of Agricultural Science
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• v.22 no.1
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• pp.69-81
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• 1995

This study was conducted to examine the genetic variants of the blood proteins and enzymes in beef cattle breeds, Hereford, Angus and Sharolais reared at the Daekwanryuong Branch of the National Livestock Research Institute. Genetic polymorphisms of transferrin(Tf), post-transferrin2(pTf-2), albumin(Alb), post-albumin (pAlb), ceruloplasmin(Cp), amylase-I(Am-I) and hemoglobin(Hb) in blood were analyzed by the methods of PAGE(polyacrylamide gel electrophoresis) and STAGE(starch gel electrophoresis). The results obtained from this study were summarized as follows: 1. Tf and pTf-2 locus assumed to be controlled by codominant alleles, A. $D_1$, $D_2$ and E allele for Tf, F and S allele for pTf-2. In genotype frequencies, 25% and 90% for Tf $D_1D_2$ and pTf-2 SS in Hereford, 25% and 100% for Tf $AD_1$ and pTf-2 FF in Angus, 50% for Tf $D_1D_1$ and pTf-2 FS in Sharolais were found to have the highest frequency, respectively. In gene frequencies, 0.400 and 0.900 for Tf E and pTf-2 S allele in Hereford, 0.678 and 0.607 for Tf $D_1$ and pTf-2S in Sharolais were appeared to have the highest frequency. 2. Alb and pAlb locus assumed to be controlled by codominant alleles, only A allele for Alb, F and S allele for pAlb. In genotype frequencies, 70% for pAlb SS in Hereford, 90% for pAlb FF in Angus and 57.15% for pAlb SS in Sharolais were found to have the highest frequency. In gene frequencies, 0.825 and 0.750 for pAlb S in Hereford and Charolais, 0.900 for pAlb F in Angus were found to have the highest frequency. 3. Cp and Am-I locus appeared to be controlled by two alleles, F and S allele for Cp, B and C allele for Am-I. In genotype frequencies, 100% and 65% for Cp FF and Am-I BB in Hereford, 45% and 85% for Cp FF, and Am-I CC in Angus, 50% and 64.29% for Cp FF and Am-I BC in Sharolais were found to have the highest frequency. Gene frequencies were 1,000, 0.600 and 0.750 for Cp F in Herehord, Angus and Sharolais, 0.800, 0.875 and 0.680 for Am-I B, C and C allele in Hereford, Angus and sharolais, respectively. 4. Hb locus assumed to be controlled by codominant alleles, only A allele in Hereford and Angus, A and B allele in Sharolais. Genotype frequencies were 57.14% and 42.86% for Hb AA and AB in Sharolais, and gene frequencies were 0.785 and 0.215 for Hb A and B in Sharolais.

• Horticultural Science & Technology
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• v.33 no.1
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• pp.93-105
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• 2015

This study was performed to analyze genetic relationships of the four major cucurbitaceous crops including watermelon, melon, cucumber, and squash/pumpkin. Among 120 EST-SSR primer sets selected from the International Cucurbit Genomics Initiative (ICuGI) database, PCR was successful for 51 (49.17%) primer sets and 49 (40.8%) primer sets showed polymorphisms among eight Cucurbitaceae accessions. A total of 382 allele-specific PCR bands were produced by 49 EST-SSR primers from 24 Cucurbitaceae accessions and used for analysis of pairwise similarity and dendrogram construction. Assessment of the genetic relationships resulted in similarity indexes ranging from 0.01 to 0.85. In the dendrogram, 24 Cucurbitaceae accessions were classified into two major groups (Clade I and II) and 8 subgroups. Clade I comprised two subgroups, Clade I-1 for watermelon accessions [I-1a and I-1b-2: three wild-type watermelons (Citrullus lanatus var. citroides Mats. & Nakai), I-1b-1: six watermelon cultivars (Citrullus lanatus var. vulgaris S chrad.)] a nd C lade I -2 for melon and cucumber accessions [I-2a-1 : 4 melon cultivars(Cucumis melo var. cantalupensis Naudin.), I-2a-2: oriental melon cultivars (Cucumis melo var. conomon Makino.), and I-2b: five cucumber cultivars (Cucumis sativus L.)]. Squash and pumpkin accessions composed Clade II {II-1: two squash/ pumpkin cultivars [Cucurbita moschata (Duch. ex Lam.)/Duch. & Poir. and Cucurbita maxima Duch.] and II-2: two squash/pumpkin cultivars, Cucurbita pepo L./Cucurbita ficifolia Bouche.}. These results were in accordance with previously reported classification of Cucurbitaceae species, indicating that watermelon EST-SSRs show a high level of marker transferability and should be useful for genetic study in other cucurbit crops.

• Journal of the Mineralogical Society of Korea
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• v.19 no.3 s.49
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• pp.171-187
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• 2006

The status of heavy metal contamination was investigated using chemical analyses of stream waters and sediments obtained from Samsanjeil and Sambong Cu mining area in Goseong-gun, Gyeongsangnam-do. In addition, the degree and the environmental risk of heavy metal contamination in stream sediments was assessed through pollution index (Pl) and danger index (DI) based on total digestion by aqua regia and fractionation of heavy metal contaminants by sequential extraction, respectively. Not only the degree of heavy metal contamination was significantly higher in Samsanjeil area than in Sambong area, but its environmental risk was also revealed much more serious in Samsanjeil area than in Sambong area. The differences in status and level of contamination and environmental risk between both two mining areas may be attributed to existence of contamination source and geology. Acid mine drainage is continuously discharged and flows into the stream in Samsanjeil mining area, and it makes the heavy metal contamination in the stream more deteriorated than in Sambong mining area in which acid mine drainage is not produced. In addition, the geology of Samsanjeil mining area is mainly comprised of andesitic rocks including a small amount of calcite and having lower pH buffering capacity fer acid mine drainage, and it is likely that the heavy metal contamination cannot be naturally attenuated in streams. On the contrary, the main geology of Sambong mining area consists of pyroclastic sedimentary Goseong formation containing a high content of carbonates, particularly calcite, and it seems that these carbonates of high pH buffering capacity prevent the heavy metal contamination from proceeding downstream in stream within that area.

• Journal of Life Science
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• v.14 no.2
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• pp.275-279
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• 2004

Gene polymorphisms of cytokines and their receptors are attractive candidates as genetic factors in the pathogenesis of immune-mediated diseases and have been reported to be associated with disease susceptibility to autoimmune, inflammatory and infectious diseases. IL-29 is one of important candidate genes for complex trait of genetic diseases but there is no published survey of single nucleotide polymorphisms (SNPs) in this gene. In this study, for the first time, we have examined the full genomic sequence of IL-29 including the promoter regions to identify SNPs. We examined the frequencies of genotypes and alleles at the SNP site of IL-29 in allergic rhinitis patients and non-allergic rhinitis controls using the direct sequencing method to determine whether this IL-29 SNP is associated with allergic rhinitis in Korean population. We identified one novel SNP (1184C＞A) in the intron 2 and one novel variation site (-1842_-1841dupGA) in the promoter region of human IL-29 gene. The P values of SNP or variation site were not significant between the healthy controls and allergic rhinitis patients. Our results suggest that the 1184C＞A polymorphism and -1842_-1841dupGA variation site in human IL-29 gene were not associated to allergic rhinitis.

• Horticultural Science & Technology
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• v.28 no.4
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• pp.627-637
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• 2010

The consumption of tomato has greatly increased recently in Korea, and a large number of tomato cultivars are commercially available in the market. However, identification of tomato cultivars by morphological traits is extremely difficult because of the narrow genetic diversity of breeding lines. Therefore, it is necessary to develop molecular markers for cultivar identification in tomato. In this study, we surveyed single nucleotide polymorphism (SNP), and developed SNP marker sets for tomato cultivar identification. SNP markers were developed based on conserved ortholog set II (COSII) and intron-based markers derived from pepper EST sequences, and marker polymorphism was tested using high-resolution melting (HRM) analysis. A total of 628 primer sets was tested, and 417 primer sets amplifying single bands were selected. Of the 417 primer sets, 70 primer sets showing HRM polymorphism among 4 inbred lines were selected. Eleven markers were selected from the 70 primer sets and subjected to cultivar identification analysis. Thirty two commercial tomato cultivars were successfully identified using the marker set.

• Journal of Life Science
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• v.20 no.3
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• pp.462-465
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• 2010

Sweetness plays an important role in providing calories and promoting appetite for food. Since it has been known that genetic factor(s) is involved in individual differences in taste sensitivity in humans, this study aimed to examine genetic variations of the TAS1R2 gene, one of the components for tasting sweet compounds, by using DNA sequencing analysis from 98 unrelated Korean subjects. As a result, 12 different single nucleotide polymorphisms (SNPs) were identified in the hTAS1R2 gene and most of them were nonsynonymous. Also, two novel SNPs were found for the first time in this study. It was noted that the frequencies of these SNPs were common in the Korean population. 20 different haplotypes with coding SNPs (cSNPs) were also found in this study. Three out of these haplotypes were common, showing frequencies of > 10%. The repertoire and frequencies of cSNPs and haplotypes in the hTAS1R2 gene will provide information that will help identify a functional ligand receptor common in the Korean population.

• Korean Journal of Breeding Science
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• v.40 no.4
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• pp.387-393
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• 2008

Over 7 individual rice (Oryza sativa L.) plants per a line were sowed and sampled by pooled sampling method for genomic DNA extraction. The 5,400 flanking sequence tags (FSTs) were analysed by adaptor PCR and direct sequencing. FST analysis showed that the intragenic FSTs, the intergenic FSTs, and the original insertional sequences including hot spot covered 48.1% (2,597), 25.6% (1,383), and 25% (1,350), respectively. The 2,597 intragenic FSTs were used for genotyping to determine whether they are heterozygous or homozygous, and 1,393 core lines were selected. Among them, 422 knockout genes were distributed on chromosome 3, while 56 - 157 intragenic FSTs scattered on other chromosomes. Among 1,393 FSTs, known genes such as transcription factor covered 59.4% (827), while unknown genes such as expressed protein covered 40.6% (566). RT-PCR indicated that some core lines had no expression or decreased expression level in their knockout genes. It means that core lines are very useful knockout lines for functional genomic studies.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.15 no.2
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• pp.78-86
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• 2015

Purpose: Homocystinuria (OMIM#236200) is a metabolic disease caused by mutation in the CBS gene. This study was conducted to identify the clinical features and prognosis of homocystinuria as well as to find out the CBS gene mutations of the six homocystinuria patients who were receiving treatment in the Pediatric Department at Soonchunhyang University Hospital. Methods: From January 1992 to March 2015, clinical, biochemical, and genetic analyses were performed retrospectively on the six patients diagnosed with classic homocystinuria at Soonchunhyang University Hospital. Results: A total of six patients were included in this study, including three who were diagnosed with homocystinuria at the mean age of $50{\pm}22.5$ days based on their abnormal newborn screening test results. The other three were diagnosed at the mean age of 7, when they visited the hospital for evaluation of developmental delay and lens dislocation. The group diagnosed at early infancy had normal cognitive function, but the other group had varying degrees of mental retardation. Major complications were found only in the group diagnosed after infancy. CBS gene mutation was found in all the patients, and they were all non-responsive to vitamin B6 treatment. At present, all patients' diets are controlled following a methionine-free formula and they are on medication with folic acid, betaine, pyridoxine, and methylcobalamin. Conclusion: Six homocystinuria patients were monitored for up to 23 years. The group diagnosed at early infancy exhibited no major complications. Therefore, early diagnosis is crucial in the prognosis, and homocystinuria must be included in the newborn screening program.