• KOREAN JOURNAL OF CROP SCIENCE
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• v.69 no.2
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• pp.111-122
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• 2024

This study was conducted to evaluate agronomic traits and classify phylogenetic characteristics of Korean wheat landraces (KWLs) collected in Gyeongnam province. We used the squash method for chromosome observation, image analysis to examine seed characteristics, and genotyping using commercial single-nucleotide polymorphism chips to construct a phylogenetic tree. All KWLs contained 42 chromosomes and two pairs of microsatellites as observed in Keumgang, a Korean wheat cultivar. All KWLs showed smaller seed traits compared with those of Keumgang, although KWL-3 had a larger embryo length than that of Keumgang. Among agronomic traits compared with those of Keumgang, all KWLs had a late heading date and ripening period except for KWL-3, which showed the smallest culm and spike length. KWL-1 had the lowest tiller, highest floret, and grain number. All KWLs showed a lower thousand grain weight than that of Keumgang because of their smaller seeds. In the variation of variety and area, the heading date, ripening period, tiller number, and floret number were affected by the cultivation area, whereas the culm length, spike length, and 1000 grain weight were affected by the variety. Correlation distribution analysis showed differences in agronomic traits according to the cultivation area, and the heading date was positively correlated with the culm length and floret number in three cultivation areas. Principal component analysis explained that the heading date had a positive relationship with the ripening period and floret number and a negative relationship with the tiller number. Principal component analysis also revealed that all KWLs had a lower thousand grain weight than that of Keumgang. Phylogenetic tree showed that KWL-1 was near KWL-3, while KWL-2 was near KWL-4. All KWLs were genetically near the Korean wheat cultivars milsung and saeol, whereas they were genetically far from the Korean wheat cultivars goso and olgrue.

• Journal of Life Science
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• v.28 no.3
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• pp.314-319
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• 2018

We analyzed QTLs for alkali-related digestion by using 120 population crossed Cheongcheong and Nagdong derived from anther culture (CNDH). The DNA markers located in the QTLs gene were selected and applied to existing cultivars. As a result of the investigation of the alkali decay degree, brown rice of Cheongcheong and Nagdong was 1.9 and 1.6, respectively, and the CNDH was $3.79{\pm}2.01$, and the distribution of variance was distributed to 7.0-1.0. The milled rice of Cheongcheong and Nagdong was 5.6 and 4.1, respectively. The mean of the CNDH was $4.86{\pm}1.55$, and the distribution of variance was distributed to 7.0-2.0. Variation distribution curves showed continuous variation that was close to non-normal distribution. In the QTLs analysis, qBRA2, qBRA6, and qBRA11 were mapped in 1-2 replications of brown rice. QHRA2-1, qHRA2-2, qHRA2-3, qHRA3, and qHRA8 were mapped in the first replication. QHRA2-1, qHRA2-2, qHRA2-3 and qHRA3 were mapped in the second replicates. And mapped to qHRA5 in 4 replicates. These were found on chromosome 2, 3, 6, 8 and 11, respectively. The phenotypic variations of qBRA2, qBRA6, and qBRA11 on the chromosomes of brown and milled rice were 1-9%. The polymorphism was analyzed for 12 types of the japonica type and six types of the indica type, based on the nine markers found in the QTLs analysis of alkali digestion. Chromosome 11, RM27258, was selected to determine the segregation ratio, which shows the difference in size by the band pattern. The results of this study will be used as basic data for the development of high-quality rice cultivars.

• The Korean Journal of Nuclear Medicine
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• v.35 no.5
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• pp.313-323
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• 2001

Purpose: The purpose of this study was to search activated genes that could be related to radiation adaptive response (RAR) induced by low-level radiation from $^{99m}Tc$ in human cell lines. Methods: We used gene discovery array (GDA) and representational difference analysis (RDA) methods. $^{99m}Tc$-pertechnetate was added to $2{\times}106/mL$ NC-37 cells (human lymphoblastic cells) to make concentrations ranging from 148 MBq/mL to 148 Bq/mL by serial 10 fold dilutions. After 44 hours, 2 Gy gamma irradiation was given to them using a Cs-137 cell irradiator. Results: As compared to the control (Con) group to which no $^{99m}Tc$ was added, those cells to which 148 and 14.8 KBq of $^{99m}Tc$ were added showed significantly lower damage to chromosomes, which was evaluated by metaphase analysis. Cells with 148 KBq $^{99m}Tc$ (T148 group) showed most significant protection. Activated genes in the T148 group as compared to Con group were evaluated by GDA and GDA methods. GDA revealed genes of casein kinase 2 (CK2) beta chain, immunoglobulins (lg), human leukocyte antigen (HLA)-B, and two novel genes. Twenty RAR related clones were selected by RDA method. The size of those genes was from 234 to 603 base pairs. Conclusions: RAR was induced by low dose irradiation from $^{99m}Tc$ in NC-37 cell lines. Genes related to the response included CK2, lg, HLA-B in human lymphoblastic cell lines.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.65 no.3
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• pp.172-181
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• 2020

Koshihikari has been one of the most popular rice cultivars with good eating quality since the 1960s despite its susceptibility to blast disease and lodging. To map the genes controlling blast resistance and to develop promising blast-resistant breeding lines inheriting Koshihikari's high eating quality, a recombinant inbred line (RIL) population was developed from a cross between Koshihikari and a blast resistance donor with early maturity, Baegilmi. A total of 394 Koshihikari × Baegilmi RILs (KBRIL), and the two parents, were evaluated for blast resistance and major agronomic traits including heading date, culm length, panicle length, and tiller number. A linkage map encompassing 1,272.7 cM was constructed from a subset of the KBRIL (n = 142) using 130 single nucleotide polymorphisms. Two quantitative trait loci (QTL) for blast resistance, qBL1.1 harboring Pish/Pi35 and qBL2.1 harboring Pib, were mapped onto chromosomes 1 and 2, respectively. qBL1.1 was detected in both of the experimental sites, Namwon and Jeonju, while qBL2.1 was only detected in Namwon. qBL1.1 and qBL2.1 did not affect agronomic traits, including heading date, culm length, panicle length, and tiller number. From the 394 KBRILs, lines that were phenotypically similar to Koshihikari were selected according to heading date and culm length and were further divided into the following two groups based on blast resistance: Koshishikari-type blast resistant lines (KR, n = 15) and Koshishikari-type blast susceptible lines (KS, n = 15). Although no significant differences were observed in the major agronomic traits between the two groups, the KR group produced a greater mean head rice ratio than the KS group. The present study provides useful materials for developing blast-resistant cultivars that inherit both Koshihikari's high eating quality and Baegilmi's blast resistance.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.65 no.4
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• pp.303-313
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• 2020

Rice grain shape is one of the key components of grain yield and market value. An understanding of the genetic basis of the variation in grain shape could be used to improve grain shape. In this study, we developed a total of 265 F₂ individuals derived from a cross between japonica cultivars (Josaeng-jado and Langi) and used this population for quantitative trait locus (QLT) analysis. Correlation analysis was performed to identify relationships between grain traits (GL: grain length, GW: grain width, L/W: ratio of length to width, TGW: 1,000 grain weight). The grain shape was positively correlated with GL and TGW, and negatively correlated with GW. In QTL analysis associated with grain shape, one QTL for GL, qGL5, detected on chromosome 5, explained 20.3% of the phenotypic variation (PV), while two QTLs, qGW5 (PV=36.1) and qGW7 (PV=26.1), for GW were identified on chromosomes 5 and 7, respectively. Evaluation of the effects of each of the QTLs on the grain shape in the population showed a significant difference in the grain size in positive lines compared with the lines without the QTLs. According to the QTL combination of the allelic-types, the grain shape of the tested lines varied from semi-round type to long spindle-shaped type. The results of this study extend our knowledge about the genetic pool governing the diversity of grain shape in japonica cultivars and could be used to improve the grain shape of this species through marker-assisted selective breeding in Korea.

• 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.

• Korean Journal of Plant Tissue Culture
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• v.24 no.1
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• pp.1-35
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• 1997

Fertilized egg, by successive cell divisions, differentiates into different tissues and organs with various structures and functions. Different cells and tissues contain different proteins, products of selective gene expression. Not all the genes in any genomes are equally active, temporal and spatial gene expression being the general rule. Present paper attempts to review the tanscriptional mechanisms or the initiations of transcription from several angles. In some of the organisms the genes in the process of transcription or the genes in the inactive state can be seen under the light microscope. Some bands of Drosophila polytene chromosomes may exhibit a swollen or puff appearance under certain conditions. A puff, unfolded or decondensed form of chromomere, represents sets of intense transcriptional activity or RNA synthesis. The heterochromatic X chromosome whose genes remain inactive in the female mammals can be visualized as a dark staining structure called Barr body, Configuration of chromatin differs between transcribed and nontranscribed chromatin. Modification to the chromatin facilitates RNA synthesis. The movement of large polymerase molecule along the DNA would probably be facilitated if some modifications of the chromatin configuration is effected. Methylation of cytosines in CG sequences is associated with inactive genes. Methylation can play a role in determination of mammalian cells during embryogenesis. Demethylation is necessary for the gene to be expressed during development A histone modification that is also known to be correlated with transcriptional capacity of chromatin is acetylation of the lysine residues of the core histones. Chromatin containing a high level of histone acetylation is very sensitive to DNase 1. For the transcription to occur TBP must first bind to the TATA box. Another TF, TF IIB, then binds to the promoter-TBP complex, facilitating the access of RNA polymerase to the transcription initiation site. As recently as eight years ago researchers assumed that histones were irrelevant to the regulation of gene expression. Histones combine with the DNA to form nucleosome of the chromatin. Histones are vital participant in gene regulation. Histone and basal factors compete for access to TATA box. When DNA is exposed to basal factors before histones are introduced, the basal factors assemble on TATA boxes preventing the access of histones, allowing transcription to occur, for transcription to begin, activator protein at the upstream activation sequence or enhancer must interact with the tail of histone H4 at TATA box and cause the histone role particle to dissociate from the TATA box leading to partial breakup of the histone core particle and allowing the basal factors to bind to the TATA box. New concept of genomic flux in contrast to the old concept of static genome has been developed based on the powerful new molecular techniques. Genomic changes such as repetitive DNAs and transposable elements, it is assumed but not yet proved, may affect some of the developmental patterns that characterize particular cells, tissues, organs, and organisms. In the last decade or so remarkable achievement have been made in the researches of the structures and functions of TFs and the specific target sequences located in promoters or enhancers where these TFs bind. TFs have independent domains that bind DNA and that activate transcription. DNA binding domain of TFs serves to bring the protein into the right location. There are many types of DNA binding domains. Common types of motifs can be found that are responsible for binding to DNA. The motifs are usually quite short and comprise only a small part of the protein structure. Steroid receptors have domains for hormone binding, DNA binding, and activating transcription. The zinc finger motif comprises a DNA binding domain. Leucine zipper consist of a stretch of amino acids with a leucine residue in every seventh position Two proteins form a dimer because they interact by means of leucine zippers on similar α-helical domain. This positions their DNA binding basic domains for interaction with the two halves of a DNA sequence with dyad symmetry of TGACTCA, ACTGAGT.

• Horticultural Science & Technology
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• v.28 no.6
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• pp.996-1002
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• 2010

Flow cytometry (FCM) was used to measure the ploidy level of three different sports from 'Campbell Early' ($Vitis$ $labruscana$) grape. Results of the study showed different ploidy levels. FCM analysis for 'Campbell Early' grape which contains 2C DNA diploid cells showed single peak around 35-40 while 'Kyoho' grape with 4C DNA tetraploid cells had a different level of 70-80. However, analysis of the sports displayed a histogram with 2 peaks containing both 2C and 4C nuclei. There was no difference in histograms of 2C DNA flesh and pericarp; on the other hand, 4C DNA flesh type of sports had a different histogram from that of the 2C DNA pericarp. Chromosome numbers of diploid ('Campbell Early'), tetraploid ('Kyoho'), and three sports were counted under the microscope. 'Campbell Early' and 'Kyoho' have 38 and 76 chromosomes, respectively. Three different sports are mixoploids with mixtures of diploid and tetraploid cells. Microscopic observations of shoot apical meristems in sports from 'Campbell Early' grape were carried out to determine the type of plant chimera. 'Campbell Early' grape (diploid) and 'Kyoho' grape (tetraploid) showed that both had 2 tunica layers covering corpus cells, while the three different sports had tunica layers showing mostly oblique division. Most cells from 'Kyoho' grape were larger than 'Campbell Early' grape. Cells from L-2 and L-3 layers of the three sports were similar to 'Kyoho' grape in size, although all cells in L-1 surface layer were uniform in size like 'Campbell Early' grape. Results of FCM analysis indicated that both normal and polyploid cells could be intermixed in sports and could become mixoploidy consisting of diploid and tetraploid. All sports used in the tests were periclinal chimera plants with two distinct L-1 and L-2 cell layers. The result of this study suggests that all three sports which originated from 'Campbell Early' grape might be 2-4-4 type chimera formation.

• Journal of Animal Science and Technology
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• v.54 no.5
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• pp.323-329
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• 2012

Genome-wide association study was performed on data from 266 Hanwoo steers derived from 66 sires using bovine 10K mapping chip in Hanwoo (Korean cattle). SNPs were excluded from the analysis if they failed in over 5% of the genotypes, had median GC scores below 0.6, had GC scores under 0.6 in less than 90% of the samples, deviated in heterozygosity more than 3 standard deviations from the other SNPs and were out of Hardy-Weinberg equilibrium for a cut-off p-value of $1^{-15}$. Unmapped and SNPs on sex chromosomes were also excluded. A total of 4,522 SNPs were included in the analysis. To test an association between SNP and QTL, a single marker regression analysis was implemented in this study. SNP was assumed to be in LD with QTL in close proximity and the effect evaluated was additive effect (QTL allele substitution effect). The number of significant SNP at a threshold of P<0.001 was 3, 5, 5 and 4 loci for live weight at 6, 12, 18 and 24 months, respectively. For live weight at different ages, significant SNP were spread out across chromosome but some of significant SNP (rs29012453 and rs29012456 on BTA24) had shown highly significant effects. As for the distribution of size of SNP effects, few loci for live weight at different age had moderate effects (6~11%) but most of significant loci had small effects (2 to 5% of additive genetic variance) against total additive genetic variance. In conclusion, live weight at different age might be affected by few loci with moderate effect and many loci with small effects across genome in Hanwoo.

• Journal of Intelligence and Information Systems
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• v.17 no.4
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• pp.241-254
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• 2011

Financial time-series forecasting is one of the most important issues because it is essential for the risk management of financial institutions. Therefore, researchers have tried to forecast financial time-series using various data mining techniques such as regression, artificial neural networks, decision trees, k-nearest neighbor etc. Recently, support vector machines (SVMs) are popularly applied to this research area because they have advantages that they don't require huge training data and have low possibility of overfitting. However, a user must determine several design factors by heuristics in order to use SVM. For example, the selection of appropriate kernel function and its parameters and proper feature subset selection are major design factors of SVM. Other than these factors, the proper selection of instance subset may also improve the forecasting performance of SVM by eliminating irrelevant and distorting training instances. Nonetheless, there have been few studies that have applied instance selection to SVM, especially in the domain of stock market prediction. Instance selection tries to choose proper instance subsets from original training data. It may be considered as a method of knowledge refinement and it maintains the instance-base. This study proposes the novel instance selection algorithm for SVMs. The proposed technique in this study uses genetic algorithm (GA) to optimize instance selection process with parameter optimization simultaneously. We call the model as ISVM (SVM with Instance selection) in this study. Experiments on stock market data are implemented using ISVM. In this study, the GA searches for optimal or near-optimal values of kernel parameters and relevant instances for SVMs. This study needs two sets of parameters in chromosomes in GA setting : The codes for kernel parameters and for instance selection. For the controlling parameters of the GA search, the population size is set at 50 organisms and the value of the crossover rate is set at 0.7 while the mutation rate is 0.1. As the stopping condition, 50 generations are permitted. The application data used in this study consists of technical indicators and the direction of change in the daily Korea stock price index (KOSPI). The total number of samples is 2218 trading days. We separate the whole data into three subsets as training, test, hold-out data set. The number of data in each subset is 1056, 581, 581 respectively. This study compares ISVM to several comparative models including logistic regression (logit), backpropagation neural networks (ANN), nearest neighbor (1-NN), conventional SVM (SVM) and SVM with the optimized parameters (PSVM). In especial, PSVM uses optimized kernel parameters by the genetic algorithm. The experimental results show that ISVM outperforms 1-NN by 15.32%, ANN by 6.89%, Logit and SVM by 5.34%, and PSVM by 4.82% for the holdout data. For ISVM, only 556 data from 1056 original training data are used to produce the result. In addition, the two-sample test for proportions is used to examine whether ISVM significantly outperforms other comparative models. The results indicate that ISVM outperforms ANN and 1-NN at the 1% statistical significance level. In addition, ISVM performs better than Logit, SVM and PSVM at the 5% statistical significance level.