• Korean Journal of Plant Resources
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• v.32 no.4
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• pp.303-311
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• 2019

Various colors of fruit skin and flesh are the most popular commercial criteria for peach classification. In order to breed new red-fleshed peach cultivar, many cross seedlings and generations should be maintained. Therefore it is necessary to develop early selection markers to screen seedlings with target traits to increase breeding efficiency. For the comparison of transcription profiles in peach cultivars differing in flesh color expression, two cDNA libraries were constructed. Differences in gene expression between red-fleshed peach cultivar, 'Josanghyeoldo' and white-fleshed peach cultivar, 'Mibaekdo' were analyzed by next-generation sequencing (NGS). Expressed sequence tag (EST) of clones from the two cultivars were selected for nucleotide sequence determination and homology searches. Putative single nucleotide polymorphisms (SNP) were screened from peach EST contigs by high resolution melting (HRM) analysis displayed specific difference between 8 red-fleshed peach cultivars and 24 white-fleshed peach cultivars. All 72 pairs of SNPs were discriminated and the HRM profiles of amplicons were established. In the study reported here, the development of SNP markers for distinguishing between red and white fleshed peach cultivars by HRM analysis offers the opportunity to use DNA markers. This SNP marker could be useful for peach marker assisted breeding and provide a good reference for relevant research on molecular mechanisms of color variation in peach cultivars.

• Korean Journal of Plant Resources
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• v.34 no.5
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• pp.443-450
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• 2021

Peach flesh color is commercially important criteria for classification and has implications for nutritional quality. To breed new yellow-fleshed peach cultivar many cross seedlings and generations should be maintained. Therefore it is necessary to develop early selection molecular markers for screening cross seedlings and germplasm with economically important traits to increase breeding efficiency. For the comparison of transcription profiles in peach varieties with a different flesh color expression, two cDNA libraries were constructed. Differences in gene expression between yellow-fleshed peach cultivar, 'Changhowon Hwangdo' and white-fleshed peach cultivar, 'Mibaekdo' were analyzed by next-generation sequencing (NGS). Expressed sequence tag (EST) of clones from the two varieties was selected for nucleotide sequence determination and homology searches. Putative single nucleotide polymorphisms (SNPs) were screened from peach EST contigs by high resolution melting (HRM) analysis, SNP ID ppa002847m:cds and ppa002540m:cds displayed specific difference between 17 yellow-fleshed and 21 white-fleshed peach varieties. The SNP markers for distinguishing yellow and white fleshed peach varieties by HRM analysis offers the opportunity to use early selection. This SNP markers could be useful for marker assisted breeding and provide a good reference for relevant research on molecular mechanisms of color variation in peach varieties.

• Animal Bioscience
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• v.36 no.7
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• pp.991-1002
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• 2023

Objective: This study aimed to elucidate the underlying gene regions responsible for productive, phenotypic or adaptive traits in different ecological types of Tibetan sheep and the discovery of important genes encoding valuable traits. Methods: We used whole-genome resequencing to explore the genetic relationships, phylogenetic tree, and population genetic structure analysis. In addition, we identified 28 representative Tibetan sheep single-nucleotide polymorphisms (SNPs) and genomic selective sweep regions with different traits in Tibetan sheep by fixation index (Fst) and the nucleotide diversity (θπ) ratio. Results: The genetic relationships analysis showed that each breed partitioned into its own clades and had close genetic relationships. We also identified many potential breed-specific selective sweep regions, including genes associated with hypoxic adaptability (MTOR, TRHDE, PDK1, PTPN9, TMTC2, SOX9, EPAS1, PDGFD, SOCS3, TGFBR3), coat color (MITF, MC1R, ERCC2, TCF25, ITCH, TYR, RALY, KIT), wool traits (COL4A2, ERC2, NOTCH2, ROCK1, FGF5, SOX9), and horn phenotypes (RXFP2). In particular, a horn-related gene, RXFP2, showed the four most significantly associated SNP loci (g. 29481646 A>G, g. 29469024 T>C, g. 29462010 C>T, g. 29461968 C>T) and haplotypes. Conclusion: This finding demonstrates the potential for genetic markers in future molecular breeding programs to improve selection for horn phenotypes. The results will facilitate the understanding of the genetic basis of production and adaptive unique traits in Chinese indigenous Tibetan sheep taxa and offer a reference for the molecular breeding of Tibetan sheep.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.54 no.4
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• pp.441-451
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• 2009

In this study, 29 simple sequence repeat (SSR) markers were used to analyze the genetic diversity and population structure of 125 rice accessions from 40 different origins in Africa, Asia, Europe, South America, and Oceania. A total of 333 alleles were detected, with an average of 11.5 per locus. The mean values of major allele frequency, expected heterozygosity, and polymorphism information content (PIC) for each SSR locus were 0.39, 0.73, and 0.70, respectively. The highest mean PIC was 0.71 for Asia, followed by 0.66 for Africa, 0.59 for South America, 0.53 for Europe, and 0.47 for Oceania. Model-based structure analysis revealed the presence of five subpopulations, which was basically consistent with clustering based on genetic distance. Some accessions were clearly assigned to a single population in which >70% of their inferred ancestry was derived from one of the model-based populations. In addition, 12 accessions (9.6%) were categorized as having admixed ancestry. The results could be used to understanding the genetic structure of rice cultivars from these regions and to support effective breeding programs to broaden the genetic basis of rice varieties.

• Parasites, Hosts and Diseases
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• v.51 no.6
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• pp.651-656
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• 2013

Human schistosomiasis caused by Schistosoma japonicum and Schistosoma mekongi is a chronic and debilitating helminthic disease still prevalent in several countries of Asia. Due to morphological similarities of cercariae and eggs of these 2 species, microscopic differentiation is difficult. High resolution melting (HRM) real-time PCR is developed as an alternative tool for the detection and differentiation of these 2 species. A primer pair was designed for targeting the 18S ribosomal RNA gene to generate PCR products of 156 base pairs for both species. The melting points of S. japonicum and S. mekongi PCR products were $84.5{\pm}0.07^{\circ}C$ and $85.7{\pm}0.07^{\circ}C$, respectively. The method permits amplification from a single cercaria or an egg. The HRM real-time PCR is a rapid and simple tool for differentiation of S. japonicum and S. mekongi in the intermediate and final hosts.

• The Korean Journal of Mycology
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• v.27 no.1 s.88
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• pp.20-26
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• 1999

The specific DNA band appeared in PCR-RAPD analysis using OPO-2 primer was a very important for the researching Korean pine-mushrooms, Tricholoma matsutake. This DNA band, sequenced to be the 770 base pairs, existed as only a single copy in the whole genomic DNA's of Korean pine-mushrooms. However, this band was not presenting from the PCR-RAPD bands of other ectomycorrhyzal fungi reacted with the OPO-2 primer or the dot blots. Also, this DNA sequence was not matched with those of the other genes known by NCBI and had low homology together with sequence of other proteins compared. Those results suggested that the specific DNA band can be used as probe for identification of T. matsutake and might be related to the informations rather than the gene for the proteins with analysis of protein sequence translated from the DNA sequence.

• Microbiology and Biotechnology Letters
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• v.41 no.4
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• pp.462-468
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• 2013

Jeotgal is a generic term given to the high-salt-fermented seafood of Korea. This study aimed at developing an overview of the bacterial community present in Ojingeo-jeotgal, a highly consumed type of jeotgal, which is made with squid. Bacteria were isolated and purified from two samples on six different kinds of media and identified by 16S rRNA gene sequence analysis. Among the 121 total isolates, the most dominant genus was Bacillus, followed by coagulase-negative staphylococci (CNS) and lactic acid bacteria (LAB). CNS were detected in both samples, but LAB were observed in only a single sample. Six strains of Bacillus species inhibiting the growth of food pathogens, Staphylococcus aureus and Vibrio parahaemolyticus, were selected from the 121 isolates. These were found to inhibit the growth of both pathogens in addition to displaying proteolytic activities on media containing 6% NaCl and 2% skim milk.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.9
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• pp.3691-3696
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• 2015

Background: Cancer loci comprise heterogeneous cell populations with diverse cellular secretions. Therefore, disseminating cancer-specific or cancer-associated protein antigens from tissue lysates could only be marginally correct, if otherwise not validated against precise standards. Materials and Methods: In this study, 2DE proteomic profiles were examined from lysates of 13 lung-adenocarcinoma tissue samples and matched against the A549 cell line proteome. A549 matched-cancer-specific hits were analyzed and characterized by MALDI-TOF/MS. Results: Comparative analysis identified a total of 13 protein spots with differential expression. These proteins were found to be involved in critical cellular functions regulating pyrimidine metabolism, pentose phosphate pathway and integrin signaling. Gene ontology based analysis classified majority of protein hits responsible for metabolic processes. Among these, only a single non-predictive protein spot was found to be a cancer cell specific hit, identified as Armadillo repeat-containing protein 8 (ARMC8). Pathway reconstruction studies showed that ARMC8 lies at the centre of cancer metabolic pathways. Conclusions: The findings in this report are suggestive of a regulatory role of ARMC8 in control of proliferation and differentiation in lung adenocarcinomas.

• Korean Journal of Plant Tissue Culture
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• v.27 no.2
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• pp.77-82
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• 2000

This study was conducted to determine the inheritance of the ability of callus formation and plant regeneration in seed cultures of rice. The culturabilities of three Japonica rices,'Chucheongbyeo', 'Nagdongbyeo', and 'Daeribbyeo 1', were higher than those of Tongil type cultivars, 'Milyang 23' and 'Samgangbyeo 'The frequency for callus growth in F₂ populations of the three crosses, 'Milyang 23/Chucheongbyeo', 'Milyang 23/Daeribbyeo 1', and' Samgangbyeo/Nagdongbyeo', revealed a nearly normal distribution. The broad-sense heritability estimated from the ability of callus formation in the crosses were ranged from 83.8% to 90.1%. The frequency distribution of plant regenerability in F₂ population of 'Milyang 23/Daeribbyeo 1' showed a continuous variation. But the segregation mode of plant regenerability from seed-derived callus in the F₂ progenies of 'Milyang 23/Chucheongbyeo' and 'Samgangbyeo/Nagdongbyeo' appeared to fit the expected 3 : 1 ratio for the high and low regenerability. These results suggest that the high plant regenerability of 'Chucheongbyeo' and 'Nagdongbyeo' was regulated by a single dominant gene.

• Genomics & Informatics
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• v.6 no.2
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• pp.91-94
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• 2008

Single nucleotide polymorphisms (SNPs) are the most abundant form of human genetic variation and are a resource for mapping complex genetic traits. A genome is covered by millions of these markers, and researchers are able to compare which SNPs predominate in people who have a certain disease. The International HapMap Project, launched in October, 2002, motivated us to start the Korean HapMap Project in order to support Korean HapMap infrastructure development and to accelerate the finding of genes that affect health, disease, and individual responses to medications and environmental factors. A Korean SNP and haplotype database system was developed through the Korean HapMap Project to provide Korean researchers with useful data-mining information about disease-associated biomarkers for studies on complex diseases, such as diabetes, cancer, and stroke. Also, we have developed a series of software programs for association studies as well as the comparison and analysis of Korean HapMap data with other populations, such as European, Chinese, Japanese, and African populations. The developed software includes HapMapSNPAnalyzer, SNPflank, HWE Test, FESD, D2GSNP, SNP@Domain, KMSD, KFOD, KFRG, and SNP@WEB. We developed a disease-related SNP retrieval system, in which OMIM, GeneCards, and MeSH information were integrated and analyzed for medical research scientists. The kHapMap Browser system that we developed and integrated provides haplotype retrieval and comparative study tools of human ethnicities for comprehensive disease association studies (http://www.khapmap.org). It is expected that researchers may be able to retrieve useful information from the kHapMap Browser to find useful biomarkers and genes in complex disease association studies and use these biomarkers and genes to study and develop new drugs for personalized medicine.