• Journal of Crop Science and Biotechnology
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• v.10 no.2
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• pp.98-105
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• 2007

Phylogenetic relationships in Korean watermelons were evaluated by genetic similarity coefficients using 15 SSR(simple sequence repeat), 14 SCAR(sequence characterized amplified region) and 14 CAPS(sequence characterized amplified region) markers. The SSR markers were selected from previously reported melon and watermelon SSRs through testing polymorphisms within a set of commercial $F_1$ varieties. The SCAR and CAPS markers were developed from polymorphic AFLP(amplified fragment length polymorphism) markers between inbred lines 'BN4001' and 'BN4002'. From the AFLP analysis, 105 polymorphic fragments were identified between the inbred lines using 1,440 primer combinations of EcoRI+CNNN and XbaI+ANNN. Based on the sequencing data of these polymorphic fragments, we synthesized sequence specific primer pairs and detected clear and reliable polymorphisms in 27 primer pairs by indels(insertion/deletion) or RFLP(restriction fragment length polymorphism). A total of 43 sequence-based PCR markers were obtained and polymorphic information content(PIC) was analyzed to measure the informativeness of each marker in watermelon varieties. The average PIC value of SCAR markers was 0.41, which was similar to that of SSR markers. Genetic diversity was also estimated by using these markers to assess the phylogenetic relationships among commercial varieties of watermelon. These markers differentiated 26 Korean watermelon varieties into two major phylogenetic groups, but this grouping was not significantly correlated with their morphological and physiological characteristics. The mean genetic similarity was 66% within the complete set of 26 commercial varieties. In addition, these sequence-based PCR markers were reliable and useful to identify cultivars and genotypes of watermelon.

• Horticultural Science & Technology
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• v.29 no.4
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• pp.336-344
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• 2011

Using the abundant available information about the tomato genome, we developed DNA markers that are linked to disease resistant loci and performed marker-assisted selection (MAS) to construct multi-disease resistant lines and varieties. Resistance markers of Ty-1, T2, and I2, which are linked to disease resistance to Tomato yellow leaf curl virus (TYLCV), Tomato mosaic virus (ToMV), and Fusarium wilt, respectively, were developed in a co-dominant fashion. DNA sequences near the resistance loci of TYLCV, ToMV, and Fusarium wilt were used for primer design. Reported candidate markers for powdery mildew-resistance were screened and the 32.5Cla marker was selected. All four markers (Ty-1, T2, I2, and 32.5Cla) were converted to cleavage amplification polymorphisms (CAPS) markers. Then, the CAPS markers were applied to 96 tomato lines to determine the phenetic relationships among the lines. This information yielded clusters of breeding lines illustrating the distribution of resistant and susceptible characters among lines. These data were utilized further in a MAS program for several generations, and a total of ten varieties and ten inbred lines were constructed. Among four traits, three were introduced to develop varieties and breeding lines through the MAS program; several cultivars possessed up to seven disease resistant traits. These resistant trait-related markers that were developed for the tomato MAS program could be used to select early stage seedlings, saving time and cost, and to construct multi-disease resistant lines and varieties.

• Journal of Animal Science and Technology
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• v.64 no.5
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• pp.830-841
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• 2022

Genetic analysis has great potential as a tool to differentiate between different species and breeds of livestock. In this study, the optimal combinations of single nucleotide polymorphism (SNP) markers for discriminating the Yeonsan Ogye chicken (Gallus gallus domesticus) breed were identified using high-density 600K SNP array data. In 3,904 individuals from 198 chicken breeds, SNP markers specific to the target population were discovered through a case-control genome-wide association study (GWAS) and filtered out based on the linkage disequilibrium blocks. Significant SNP markers were selected by feature selection applying two machine learning algorithms: Random Forest (RF) and AdaBoost (AB). Using a machine learning approach, the 38 (RF) and 43 (AB) optimal SNP marker combinations for the Yeonsan Ogye chicken population demonstrated 100% accuracy. Hence, the GWAS and machine learning models used in this study can be efficiently utilized to identify the optimal combination of markers for discriminating target populations using multiple SNP markers.

• The Journal of Korean Medicine
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• v.38 no.1
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• pp.72-80
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• 2017

Objectives: The purpose of this study is to evaluate the urinary organic acid comprehensive profile for chemotherapy induced peripheral neuropathy (CIPN). Methods: Participants are 66 patients with CIPN who had symptom (Visual analog scale ${\geq}30mm$, Eastern Cooperative Oncology Group ${\leq}2$). Participants were tested with organic acid comprehensive profile markers. Results: Positive Correlation was observed in the neurotransmitter metabolism markers, N-methyl-D-aspartate (NMDA) modulators markers, detoxification markers, energy production markers, amino acid metabolism markers, and intestinal dysbiosis markers. Especially, all the neurotransmitter metabolism markers were showed positive rate of 44%. In addition, neuro-endo-immune was associated with energy metabolism (mitochondrial dysfunction) in CIPN of cancer patient. especially detoxification, intestinal bacterial hyperplasia, vitamin deficiency (folate, complex B group, vitamin C). Conclusions: Significant urinary organic acid comprehensive profile results were obtained in cancer patients who induced peripheral neuropathy by chemotherapy.

• Horticultural Science & Technology
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• v.30 no.1
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• pp.56-63
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• 2012

Tomato hypocotyl can generally be one of two colors, purple or green. Genetically, this trait is controlled by a single dominant gene. Hypocotyl tissue specific color expression is one of many visible genetic marker sources used to select tomato progeny. However, the visible marker does not show a clear distinction between homozygous genotype and heterozygous genotype from the breeding lines. Therefore, to identify a hypocotyl pigmentation related marker, we screened DNA polymorphisms in thirteen tomato lines showing purple or green hypocotyls. The markers used for screening consisted of primer set information obtained from anthocyanin related genes, conserved ortholog set II (COS II) marker sets localized near anthocyanin related genes, and restriction fragment length polymorphism (RFLP) markers localized near COS II markers, which produce polymorphisms between purple and green tomatoes. One primer from a RFLP fragment resulted in a polymorphism on agarose gel electrophoresis. From the RFLP fragment, a cleaved amplified polymorphic sequence (CAPS) marker was developed to distinguish between purple and green hypocotyls. The genotypes of 135 $F_2$ individuals were analyzed using the CAPS marker, and among them, 132 individuals corresponded to the phenotypes of hypocotyl pigmentation.

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2005.11a
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• pp.344-344
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• 2005

• Proceedings of the Korean Society of Crop Science Conference
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• 2007.11a
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• pp.219.1-219.1
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• 2007

• Journal of the Korean Society for Precision Engineering
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• v.23 no.3 s.180
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• pp.179-186
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• 2006

Single-walled carbon nanotubes (SWNT) exhibit strong Raman signals as well as fluorescence emissions in the near infrared regions where most biomolecules are transparent. Such signals do not blink or photobleach under prolonged excitation. which is advantageous to optical nano-bio marker applications. In this paper, single walled carbon nanotubes are conjugated with specific types of single-stranded DNA in order to detect oligonucleotides of corresponding complimentary sequences. Dot blotting experiments and comparative Raman spectroscopy observations demonstrated excellent sensitivity and specificity of carbon nanotube-DNA probes. The results show the possibility of using SWNT as generic nano-bio markers for the precise detection of specific kinds of genes.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.10a
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• pp.264-264
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• 2017

• Proceedings of the Korean Society of Plant Biotechnology Conference
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• 2006.06a
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• pp.25.2-26
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• 2006