• KOREAN JOURNAL OF CROP SCIENCE
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• v.57 no.1
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• pp.71-77
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• 2012

The objective of this study is to develop the gene based sequence tagged site (STS) markers in wheat. The euchromatin enriched genomic library was constructed and the STS primer sets were designed using gene based DNA sequence. The euchromatin enriched genomic (EEG) DNA library in wheat was constructed using the $Mcr$A and $Mcr$BC system in $DH5{\alpha}$ cell. The 2,166 EEG colonies have been constructed by methylated DNA exclusion. Among the colonies, 606 colonies with the size between 400 and 1200 bp of PCR products were selected for sequencing. In order to develop the gene based STS primers, blast analysis comparing between wheat genetic information and rice genome sequence was employed. The 227 STS primers mainly matched on $Triticum$ $aestivum$ (hexaploid), $Triticum$ $turgidum$ (tetraploid), $Aegilops$ (diploid), and other plants. The polymorphisms were detected in PCR products after digestion with restriction enzymes. The eight STS markers that showed 32 polymorphisms in twelve wheat genotypes were developed using 227 STS primers. The STS primers analysis will be useful for generation of informative molecular markers in wheat. Development of gene based STS marker is to identify the genetic function through cloning of target gene and find the new allele of target trait.

• Horticulture, Environment, and Biotechnology : HEB
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• v.59 no.6
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• pp.857-864
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• 2018

Previous studies have not detected transcripts of the gene encoding anthocyanidin synthase (ANS) in white pomegranates (Punica granatum L.) and suggest that a large-sized insertion in the coding region of the ANS gene might be the causal mutation. To elucidate the identity of the putative insertion, 3887-bp 5' and 3392-bp 3' partial sequences of the insertion site were obtained by genome walking and a gene coding for an expansin-like protein was identified in these genome-walked sequences. An identical protein (GenBank accession OWM71963) isolated from pomegranate was identified from BLAST search. Based on information of OWM71963, a 5.8-Mb scaffold sequence with genes coding for the expansin-like protein and ANS were identified. The scaffold sequence assembled from a red pomegranate cultivar also contained all genome-walked sequences. Analysis of positions and orientations of these genes and genome-walked sequences revealed that the 27,786-bp region, including the 88-bp 5' partial sequences of the ANS gene, might be translocated into an approximately 22-kb upstream region in an inverted orientation. Borders of the translocated region were confirmed by PCR amplification and sequencing. Based on the translocation mutation, a simple PCR codominant marker was developed for efficient genotyping of the ANS gene. This molecular marker could serve as a useful tool for selecting desirable plants at young seedling stages in pomegranate breeding programs.

• 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.

• Horticultural Science & Technology
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• v.33 no.5
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• pp.730-736
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• 2015

Tomato spotted wilt virus (TSWV) causes one of the most destructive viral diseases that threatens global tomato production. Sw-5b was reported as the resistance gene effective against TSWV. The objective of this research was to develop a single-nucleotide polymorphism (SNP) marker to distinguish tomato cultivars resistant to TSWV from susceptible cultivars for marker-assisted breeding. First, we determined genotypes for TSWV resistance in 32 commercial tomato cultivars using the previously reported Sw-5b gene-based marker. Then, DNA sequences of Sw-5b alleles in tomato cultivars showing resistant or susceptible genotypes were analyzed; a single SNP was found to distinguish tomato cultivars resistant to TSWV from susceptible cultivars. Based on the confirmed SNP, a SNP primer pair was designed. Using this new SNP sequence and high-resolution melting analysis, the same 32 tomato cultivars were screened. The results were perfectly correlated with those from screening with the Sw-5b gene-based marker. These results indicate that the SNP maker developed in this study will be useful for better tracking of resistance to TSWV in tomato breeding.

• Journal of KIISE:Computer Systems and Theory
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• v.35 no.8
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• pp.372-377
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• 2008

Multiclass cancer classification has been actively investigated based on gene expression profiles, where it determines the type of cancer by analyzing the large amount of gene expression data collected by the DNA microarray technology. Since gene expression data include many genes not related to a target cancer, it is required to select informative genes in order to obtain highly accurate classification. Conventional rank-based gene selection methods often use ideal marker genes basically devised for binary classification, so it is difficult to directly apply them to multiclass classification. In this paper, we propose a novel method for multiclass gene selection, which does not use ideal marker genes but directly analyzes the distribution of gene expression. It measures the class-discriminability by discretizing gene expression levels into several regions and analyzing the frequency of training samples for each region, and then classifies samples by using the naive Bayes classifier. We have demonstrated the usefulness of the proposed method for various representative benchmark datasets of multiclass cancer classification.

• Journal of Crop Science and Biotechnology
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• v.11 no.4
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• pp.233-236
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• 2008

A positive selectable marker system was adapted for transformation of mature embryo-derived calli of Indica rice (Oryza sativa L.) utilizing the PMI gene encoding for phosphomannose-isomerase that converts mannose-6-phosphate to fructose-6-phosphate. The transformed cells grew on medium supplemented with 3% mannose as carbon source and calli were selected on media containing various concentrations of mannose. Molecular analyses showed that the transformed plants contained the PMI gene. The results indicate that the mannose selection system can be used for Agrobacterium-mediated transformation of mature embryo in rice to substitute the use of conventional selectable markers in genetic transformation.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.56 no.4
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• pp.329-341
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• 2011

The objective of this study was to determine the genetic diversities of major rice blast resistance genes among 84 accessions of aromatic rice germplasm. Eighty four accessions were characterized by a dominant 11 set of PCR-based SNP and CAPS marker, which showed the broad spectrum resistance and closest linkage to seven major rice blast resistance (R) genes, Pia, Pib, Pii, Pi5 (Pi3), Pita (Pita-2), and Pi9 (t). The allele specific PCR markers assay genotype of SCAR and STS markers was applied to estimate the presence or absence of PCR amplicons detected with a pair of PCR markers. One indica accession, Basmati (IT211194), showed the positive amplicons of five major rice blast resistance genes, Pia, Pi5 (Pi3), Pib, Pi-ta (Pi-ta2), and Pik-5 (Pish). Among 48 accessions of the PCR amplicons detected with yca72 marker, only five accessions were identified to Pia gene on chromosome 11. The Pib gene was estimated with the NSb marker and was detected in 65 of 84 accessions. This study showed that nine of 84 accessions contained the Pii gene and owned Pi5 (Pi3) in 42 of 84 accessions by JJ817 and JJ113-T markers, which is coclosest with Pii on chromosome 9. Only six accessions were detected two alleles of the Pita or Pita-2 genes. Three of accessions were identified as the Pi9 (t) gene locus.

• The Korea Journal of Herbology
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• v.28 no.5
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• pp.1-6
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• 2013

Objectives : This study was conducted to identify the original Sinomini Caulis et Rhizoma plant among Stephania tetrandra, Cocculus trilobus, and Aristolochiae fangchi to develop the genetic marker for Sinomini Caulis et Rhizoma. Methods : Sinomenium acutum was identified by the classification and identification committee of the National Center for Standardization of Herbal Medicines. The chloroplast ndhF gene was amplified. We performed sequences alignment analysis of Sinomenium acutum, Stephania tetrandra, C. trilobus, and A. fangchi using BioEdit program. The SFR markers designed were consisted of SF01, SR04, and SR05 primers. Results : Many variations of Sinomeni Caulis et Rhizoma are currently commercialized as herbal medicine. We compared the base sequences of the ndhF intergenic space of chloroplast DNA with Sinomenium acutum, Stephania tetrandra, C. trilobus, and A. fangchi. According to the results, it showed that the nucleotide variations were seen in 30 genes of four species. Phylogenetic analysis revealed that 4 species were classified into five groups based on an inter-group divergence in nucleotide sequence of 9%. We developed SFR marker nucleotides enough to authenticate respective species and confirmed its application on the band size at 419 base pair. These sequence differences at corresponding positions were available genetic markers to identity the Sinomeni Caulis et Rhizoma. Conclusions : Base on these results, the ndhF region was effective in distinguishing Sinomini Caulis et Rhizoma The SFR genetic marker was useful for identifying Sinomini Caulis et Rhizoma with other species.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.50 no.6
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• pp.453-456
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• 2005

This study was carried out to select DNA markers closely linked to brown planthopper (BPH) resistance gene originated from a rice cultivar 'Cheongcheong­byeo'. For the mapping of resistant gene to BPH, a doubled-haploid (DH) population was developed by anther culture of $F_1$ plants from a cross 'Cheongcheong­byeo/Nagdongbyeo'. In BPH bioassay and marker screen­ing for the DH population, the segregation of resistant and susceptible plants to BPH fitted to a 1:1 ratio. A total of 310 RAPDs of 520 markers showed polymorphism in parental survey using 'Cheongcheongbyeo' and 'Nag­dongbyeo'. In the analysis of relationship between BPH resistance and marker pattern for 40 DH lines, the OPE16 produced a specific dominant fragment, 700 bp, which was closely linked with BPH resistance gene of 'Cheong­cheongbyeo'. Based on the linkage analysis using 7 markers, BPH resistance of 'Cheongcheongbyeo' was mapped on chromosome 12, which was closely linked with $OPE16_{700}$ at a distance of 4.6 cM.

• Journal of Life Science
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• v.19 no.1
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• pp.152-155
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• 2009

The old-gold-crimson ($og^c$) fruit color mutation produces deep red tomato fruit with high lycopene content. age is a null mutation allele of lycopene-${\beta}$-cyclase (Crt-b) gene (B locus) that converts lycopene to ${\beta}$-carotene in the cartenoid biosynthesis pathway in tomato. Breeding of high lycopene tomato cultivars can be accelerated by marker-assisted selection (MAS) for introgression of $og^c$ allele by using a gene-based DNA marker. In order to develop a marker, single nucleotide deletion of adenine(A) with. in a poly-A repeat that has been known to be responsible for frame-shift mutation of $og^c$ was confirmed by resequencing mutant allele and wild-type allele at B locus of several tomato lines. For allele discrimination and detection of $og^c$, derived CAPS (dCAPS) approach was used by designing a primer that artificially introduced restriction enzyme recognition site of Hin fI in PCR products from $og^c$ allele. This dCAPS marker is co-dominant gene-based PCR marker that can be efficiently used for MAS breeding program aiming the development of high lycopene tomato.