• Genomics & Informatics
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• v.11 no.4
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• pp.277-281
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• 2013

RNA analysis has become a reliable method of body fluid identification for forensic use. Previously, we developed a combination of four multiplex quantitative PCR (qRT-PCR) probes to discriminate four different body fluids (blood, semen, saliva, and vaginal secretion). While those makers successfully identified most body fluid samples, there were some cases of false positive and negative identification. To improve the accuracy of the identification further, we tried to use multiple markers per body fluid and adopted the NanoString nCounter system instead of a multiplex qRT-PCR system. After measuring tens of RNA markers, we evaluated the accuracy of each marker for body fluid identification. For body fluids, such as blood and semen, each body fluid-specific marker was accurate enough for perfect identification. However, for saliva and vaginal secretion, no single marker was perfect. Thus, we designed a logistic regression model with multiple markers for saliva and vaginal secretion and achieved almost perfect identification. In conclusion, the NanoString nCounter is an efficient platform for measuring multiple RNA markers per body fluid and will be useful for forensic RNA analysis.

• The Plant Pathology Journal
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• v.35 no.3
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• pp.200-207
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• 2019

Fusarium head blight (FHB) is a devastating wheat disease with a significant economic impact. Fhb1 is the most important large effect and stable QTL for FHB resistance. A pore-forming toxin-like (PFT) gene was recently identified as an underlying gene for Fhb1 resistance. In this study, we developed and validated a PFT-based Kompetitive allele specific PCR (KASP) marker for Fhb1. The KASP marker, PFT_KASP, was used to screen 298 diverse wheat breeding lines and cultivars. The KASP clustering results were compared with gelbased gene specific markers and the widely used linked STS marker, UMN10. Eight disagreements were found between PFT_KASP and UMN10 assays among the tested lines. Based on the genotyping and sequencing of genes in the Fhb1 region, these genotypes were found to be common with a previously characterized susceptible haplotype. Therefore, our results indicate that PFT_KASP is a perfect diagnostic marker for Fhb1 and would be a valuable tool for introgression and pyramiding of FHB resistance in wheat cultivars.

• Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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• 2011.05a
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• pp.375-377
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• 2011

The augmented reality is a technology which expresses the information hardly obtained in the real world by synthesizing virtual objects in the real world. This study uses IR LED marker to obtain the coordination of real world for registration of virtual objects. Since the IR LED marker is inserted in target object thus it has properties of invisible markers. To realize the augmented reality, the existence of marker can be observed in camera input image. Therefore, this paper provides a method to give the properties of perfect invisible marker by using inpainting technology when realizing IR LED marker.

• Language and Information
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• v.16 no.2
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• pp.43-66
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• 2012

In this paper, I attempt to define the semantics of cikum 'now' in Korean. To define it precisely, we need to look at how it interacts with different aspectual classes of verbs and with the semantics of tenses and aspects. In doing this we need to define the semantics of tenses and aspects. Here we run into the question of whether ess is a tense marker or an aspect marker. I assume that it is ambiguous. There are still cases where it is not clear whether ess is used as a tense marker or an aspect marker in an actual sentence. I discuss two such cases: one in which it is used with verbs like tochakha 'arrive' which have no salient resulting states, and one in which a state verb is used with cikum-kkaci 'until now'. The semantics of cikum can be defined differently depending on whether ess is a tense or an aspect. By discussing ko iss, which is an imperfect marker, I conclude that cikum means ${\lambda}P{\lambda}i[u{\subseteq}i{\wedge}P(i)]$, that is, a relation between a set of times which include an utterance time and a set of properties of times.

• Horticultural Science & Technology
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• v.33 no.4
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• pp.550-558
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• 2015

To analyze the linkage relationships among molecular markers recently reported to be linked to onion (Allium cepa L.) Ms, a restorer-of-fertility locus, in onion (Allium cepa L.), three single nucleotide polymorphism markers were converted into cleaved amplified polymorphic sequence (CAPS) markers based on onion transcriptome sequences and the rice genome database. Analysis of the recombinants selected from 4,273 segregating plants using CAPS and other linked markers demonstrated the jnurf13 and jnurf610 markers to perfectly co-segregate with the Ms locus. In contrast to jnurf13, the jnurf610 marker was not in perfect linkage disequilibrium with the Ms locus in diverse breeding lines. Thus, the jnurf13 marker and the marker for identification of cytoplasm types were utilized to enhance the efficiency of onion breeding through four applications. First, 89 maintainer lines containing the normal cytoplasm and homozygous recessive Ms genotypes were successfully identified from 100 breeding lines. Second, these two molecular markers were used to analyze the main sources of male-fertile contaminants frequently found in the male-sterile parental lines during F1 hybrid seed production. The majority of the contaminants contained heterozygous Ms genotypes, indicating that pollen grains harboring the dominant Ms genotype may have been introduced during propagation of the maintainer lines. Therefore, the genetic purity of the two maintainer lines was analyzed in the third application, and the results showed that both maintainer lines contained 13-21% off-types. Finally, the two markers were used to increase the seed yield potentials of two open-pollinated varieties containing sterile cytoplasms by removing the plants harboring homozygous recessive and heterozygous Ms genotypes.

• Korean Journal of Plant Resources
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• v.14 no.2
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• pp.139-147
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• 2001

This study was conducted to clarify of relationship with major physiological characters and RAPD patterns of garlic(Allium sativum L.) germplasm collected from the worldwide using randomly amplified polymorphic DNA(RAPD) analysis. Eighty-four garlic accessions were classified into ten varietal groups by physiological characters with the single linkage clustering based on Q correlations. The majority was early maturing varieties collected from East-Asia, late maturing varieties were Europe. RAPD marker, $WE61_{1,630}$ was amplified with late maturing varieties and high correlation have shown, though three accessions weren't amplified. Clove undifferentiation and secondary growth had mainly occur accessions collected from Europe, but hadn't shown perfect linkage to RAPD. RAPD marker, $WF70_{1,400}$ appeared in bolting garlic and $WF64_{1,400}$ appeared only in fertile garlic. Unknown garlic amplified in $WF64_{1,400}$ might be fertile garlic, because of their collection site were from Central-Asia.

• The Plant Pathology Journal
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• v.25 no.3
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• pp.286-290
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• 2009

The stability of three different kinds of pUC-derived plasmids, pDsRed, pZsYellow, and pGFPuv, was investigated in Pectobacterium strains to utilize those plasmids as tracers. All three plasmids pDsRed, pZsYellow and pGFPuv showed their specific colors in Pectobacterium strains. Especially, the plasmid pDsRed conferred bright pink colonies on the Pectobacterium strains. When the bacteria lost the plasmid pDsRed, the colonies turned white, suggesting that the plasmid could be a good marker system for Pectobacterium strains on different environmental conditions. The effect of the antibiotic pressure on the stability of the plasmid was different depending on the host bacteria. P. carotovorum subsp. betavasculorum was more sensitive to the antibiotic pressure than P. carotovorum subsp. carotovorum Pcc21. However, temperature change significantly affected plasmid stability on both Pectobacterium strains. Almost all strains lost the plasmids with the shift in temperature from $28^{\circ}C$ to $37^{\circ}C$. Presence of the plasmids did not affect bacterial pathogenicity on their own host plants. Among three plasmids, pZsYellow was not useful as a marker because the yellow fluorescent proteins from pZs Yellow were interfered with the yellow natural fluorescence of the plant tissues induced by the defense system. Since the red color of DsRed can be seen with naked eyes, plasmid pDsRed was applicable as a marker. However, the color change was slow so that additional manipulation to increase the expression speed was necessary. Plasmid pGFPuv could serve as a perfect marker without any problem, tracing the reproduction and spread of the plant pathogens perfectly.

• Journal of Crop Science and Biotechnology
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• v.10 no.4
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• pp.201-210
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• 2007

Soybean [Glycine max(L.) Merr.] oil is versatile and used in many products. Modifying the fatty acid profile would make soy oil more functional in food and other products. The ideal oil with the most end uses would have saturates(palmitic + stearic acids) reduced from 15 to < 7%, oleic acid increased from 23 to > 55%, and linolenic acid reduced from 8 to < 3%. Reduced palmitic acid(16:0) is conditioned by three or more recessive alleles at the Fap locus. QTLs for reduced palmitic acid have mapped to linkage groups(LGs) A1, A2, B2, H, J, and L. Genes at the Fad locus control oleic acid content(18:1). Six QTLs($R^2$=4-25%) for increased 18:1 in N00-3350(50 to 60% 18:1) explained four to 25% of the phenotypic variation. M23, a Japanese mutant line with 40 to 50% 18:1 is controlled by a single recessive gene, ol. A candidate gene for FAD2-1A can be used in marker-assisted breeding for high 18:1 from M23. Low linolenic acid(18:3) is desirable in soy oil to reduce hydrogenation and trans-fat accumulation. Three independent recessive genes affecting omega-3 fatty acid desaturase enzyme activity are responsible for the lower 18:3 content in soybeans. Linolenic acid can be reduced from 8 to about 4, 2, and 1% from copies of one, two, or three genes, respectively. Using a candidate gene approach perfect markers for three microsomal omega-3 desaturase genes have been characterized and can readily be used in for marker assisted selection in breeding for low 18:3.

• Korean Journal of Breeding Science
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• v.40 no.3
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• pp.223-227
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• 2008

In rice, tillering is an important trait determining yield. To study tillering at the agricultural and molecular aspects, we have examined a spontaneous rice mutant that showed reduction in the number of culms. The mutant was derived from a $F^6$ line of the cross of Junambyeo*4 / IR72. It could produce, on average, 4 tillers per hill in the paddy field while wild-type plants usually have 15. Except the reduced culm numbers, they also show pale green phenotypes. The phenotypes of this mutant were co-segregated as the monogenic Mendelian ratio (${\chi}^b=0.002$, p=0.969). In order to locate a gene responsible for the rcn phenotype, the mutant with the japonica genetic background was crossed with Milyang21 of the indica background. Bulked segregant analysis was used for rapid determination of chromosomal location. Three SSR markers (RM551, RM8213, and RM16467) on chromosome 4 were genetically associated with the mutant phenotype. Each of the 217 $F_2$ plants was genotyped with simple sequence length polymorphisms. The data showed that RM16572 on chromosome 4 was the closest marker that showed perfect co-segregation among the $F_2$ population. We suggest the new rcn gene studied here name as $rcn10^t$ because there was no report which exhibit a rcn phenotype with a pleiotropic effect of pale green (chlorophyll deficiency), and mapped at same position on chromosome 4.

• Genomics & Informatics
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• v.5 no.1
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• pp.1-5
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• 2007

Embryonic stem cells can be differentiated into various types of cells, requiring a tight regulation of transcription. Biomarkers related to each lineage of cells are used to guide the differentiation into neural or any other fates. In previous experiments, we reported the guided differentiation (GD)-specific genes by comparing profiles of random differentiation (RD). Interestingly 68% of differentially expressed genes in GD overlap with that of RD, which makes it difficult for us to separate the lineages by examining several markers. In this paper, we design a prediction model to identify the differentiation into neural fates from any other lineage. From the profiles of 11,376 genes, 203 differentially expressed genes between neural and random differentiation were selected by random variance T-test with 95% confidence and 5% false discovery rate. Based on support vector machine algorithm, we could select 79 marker genes from the 203 informative genes to construct the optimal prediction model. Here we propose a prediction model for the prediction of neural fates from random differentiation which is constructed with a perfect accuracy.