• Biomedical Science Letters
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• v.29 no.4
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• pp.302-313
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• 2023

Y chromosomal short tandem repeat (Y-STR) markers have been developed continuously to complement forensic DNA analyses and population genetic studies. Initially, we collected data from previously reported Korean population Y-STR haplotype studies on 1133 individuals. We then conducted a marker expansion analysis using a dataset from the Y-STR Haplotype Reference Database (YHRD), covering up to 29 Y-STRs, referred to as Ymax. Additionally, we examined the impact of rapidly mutating (RM) Y-STRs included in this expanded marker set on the discrimination capacity. We observed that marker expansions both with (0.9896), and without (0.9510), RM Y-STR improved the discrimination capacity. Subsequently, we focused on 16 individuals belonging to seven distinct groups sharing identical haplotypes. These particular haplotypes had been previously identified among 476 unrelated males using 23 Y-STR markers from the PowerPlex^® Y23 System. We expanded the marker panel up to Ymax to explore how discrimination improved with an expansion of Y-STR markers for these 16 individuals. Among the expanded markers, DYS627, which had high discriminatory power, had a high mutation rate (1.10 × 10^-2) and high gene diversity (0.83). In contrast, DYF387S1 displayed high gene diversity (0.95) but a relatively low mutation rate (2.80 × 10^-3). We propose that these findings will be valuable in the selection of suitable Y-STR markers, depending on the objectives of forensic analyses. Additionally, the presence of frequently observed Y-haplotypes in Korean population will facilitate statistical interpretation in Y-STR DNA profiling.

• Food Science of Animal Resources
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• v.31 no.4
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• pp.530-536
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• 2011

It is well established that uncoupling protein 3 (UCP3) is expressed largely in skeletal muscle, white adipose tissue and brown adipose tissue and has been suggested to play important roles in regulating energy expenditure, body weight, thermoregulation as well as fatty acid metabolism and obesity. Therefore, the UCP3 gene was selected as a candidate gene for carcass and meat quality traits in Korean cattle. The objective of this study was to identify single nucleotide polymorphisms (SNPs) in the UCP3 gene and to evaluate the association of UCP3 SNP markers with carcass and meat quality traits in Korean cattle. The five exons in the UCP3 gene were sequenced, and ten SNPs were identified. The PCR-SSCP method was then developed to genotype the individuals examined. The g.3076A>G genotype was significantly associated with marbling score (MS) of Korean cattle. Animals with the AA genotype had a higher MS than those with the AG and GG genotypes. No significant associations of the SNP g.3076A>G were observed for any traits. In conclusion, although SNP g.3076A>G, which showed an association with MS, does not cause amino acid changes, this SNP may be used as a DNA marker to select animals that have higher intramuscular fat content.

• Asian-Australasian Journal of Animal Sciences
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• v.14 no.4
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• pp.587-596
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• 2001

In the last decade, rapid developments in molecular biotechnology and of genomic tools have enabled the creation of dense linkage maps across whole genomes of human, plant and animals. Successful development and implementation of interval mapping methodologies have allowed detection of the quantitative trait loci (QTL) responsible for economically important traits in experimental and commercial livestock populations. The candidate gene approach can be used in any general population with the availability of a large resource of candidate genes from the human or rodent genomes using comparative maps, and the validated candidate genes can be directly applied to commercial breeds. For the QTL detected from primary genome scans, two incipient fine mapping approaches are applied by generating new recombinants over several generations or utilizing historical recombinants with identity-by-descent (IBD) and linkage disequilibrium (LD) mapping. The high resolution definition of QTL position from fine mapping will allow the more efficient implementation of breeding programs such as marker-assisted selection (MAS) or marker-assisted introgression (MAI), and will provide a route toward cloning the QTL.

• Applied Biological Chemistry
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• v.36 no.6
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• pp.557-561
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• 1993

The neomycin phosphotransferase II gene (nptII) was introduced into geranium (Pelargonium zonale hybrids) protoplast by using PEG or electroporation method. The presence of the introduced DNA in the protoplast and the expressions of the gene in the transformed cells were examined. The presence of the nptII DNA in the protoplasts were detected by polymerase chain reaction. The expressions of nptII gene in the transformed cells were confirmed by the nptII assay.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.46 no.5
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• pp.416-419
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• 2001

Hypernodulation soybean mutant, SS2-2, is characterized with greater nodulation and nitrogen fixing ability in the root nodule than its wild type, Shinpaldalkong 2. The present study was performed to identify a genetic locus conferring hypernodulation in soybean mutant SS2-2 and to determine whether the gene controlling the hypernodulation of SS2-2 is allelic to that controlling the supernodulation of nts382 mutant. Hybridization studies between SS2-2 and Taekwangkong revealed that the recessive gene was responsible for the hypernodulation character in soybean mutant SS2-2. Allelism was also tested by crossing supernodulating mutant nts382 and hypernodulating mutant SS2-2 that both hypernodulation and supernodulation genes were likely controlled by an identical locus. Molecular marker mapping of hypernodulation gene in SS2-2 using SSR markers confirmed that the gene conferring hypernodulation was located at the same loci with the gene conferring supernodulation. It is interesting to note that the same gene controlled the super- and hyper-nodulation characters, although SS2-2 and nts 382 exhibited differences in the amount of nodulation in the root system. Further genetic studies should be needed to clarify the genetic regulation of super- and hyper-nodulation in soybean.

• Journal of the Korea Society of Computer and Information
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• v.15 no.12
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• pp.197-207
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• 2010

Using a variety of data-mining methods on high-throughput cDNA microarray data, the level of gene expression in two different tissues can be compared, and DEG(Differentially Expressed Gene) genes in between normal cell and tumor cell can be detected. Diagnosis can be made with these genes, and also treatment strategy can be determined according to the cancer stages. Existing cancer classification methods using machine learning select the marker genes which are differential expressed in normal and tumor samples, and build a classifier using those marker genes. However, in addition to the differences in gene expression levels, the difference in gene-gene correlations between two conditions could be a good marker in disease diagnosis. In this study, we identify gene pairs with a big correlation difference in two sets of samples, build gene classification modules using these gene pairs. This cancer classification method using gene modules achieves higher accuracy than current methods. The implementing clinical kit can be considered since the number of genes in classification module is small. For future study, Authors plan to identify novel cancer-related genes with functionality analysis on the genes in a classification module through GO(Gene Ontology) enrichment validation, and to extend the classification module into gene regulatory networks.

• Biotechnology and Bioprocess Engineering:BBE
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• v.9 no.3
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• pp.217-222
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• 2004

As Agrobacterium tumefaciens, which has long been used to transform plants, is known to transfer T-DNA to budding yeast, Saccharomyces cerevisiae, a variety of fungi were subjected to the A. tumefaciens-mediated transformation to improve their transformation frequency and feasibility. The A. tumefaciens-mediated transformation of chestnut blight fungus, Cryphonectria parasitica, is performed in this study as the first example of transformation of a hardwood fungal pathogen. The transfer of the binary vector pBIN9-Hg, containing the bacterial hygromycin B phosphotransferase gene under the control of the Aspergillus nidulans trpC promoter and terminator, as a selectable marker, led to the selection of more than 1,000 stable, hygromycin B-resistant transformants per 1${\times}$10$\^$6/ conidia of C. parasitica. The putative transformants appeared to be mitotically stable. The transformation efficiency appears to depend on the bacterial strain, age of the bacteria cell culture and ratio of fungal spores to bacterial cells. PCR and Southern blot analysis indicated that the marker gene was inserted at different chromosomal sites. Moreover, three transformants out of ten showed more than two hybridizing bands, suggesting more than two copies of the inserted marker gene are not uncommon.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.40 no.3
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• pp.128-132
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• 2007

We identified a microsatellite marker, Poli121TUF, which appears to be significantly linked (P<0.001) with a lymphocystis disease virus (LCDV)-resistance gene in the olive flounder, Paralichthys olivaceus. The olive flounder is an economically important food fish, that is widely cultured in Korea, Japan, and China. Lymphocystis disease has spread in these countries and has seriously reduced the economic value of the fish. LCDV causes lymphocystis cells (LC) to form on the body surface, fins, gills, mouth, and intestine. Fish with LC lose commercial value due to their deformed appearance. The identified micro satellite marker can be used as a candidate locus for marker-assisted selection (MAS) in order to enhance the efficiency of selection for LCDV resistance in the olive flounder.

• Journal of Life Science
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• v.12 no.6
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• pp.715-720
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• 2002

A mutant Arabidopsis thaliana which is very sensitive to Ultraviolet-B(UV-B) radiation has been isolated by ethylmethane sulfonate(EMS) mutagenesis. Genetic cross proved the UV-sensitive gene(uvs) to segregate as a single Mendelian locus. For mapping of uvs, we crossed Arabidopsis thaliana Lansberg with uvs plant(Columbia), and made F2 plants by F1 selfcross. We designed 10 kinds of CAPS marker primers. Each primers amplifies a single mapped DNA sequence from uvs and Lansberg erecta ecotyres. Also identified was at least one restriction endonuclase for each of these PCR product that generates ecotype-specific digestion pattern. We got crossing over value of UB-sensitivity and each CAPS marker which located on different chromosome arm. The value of crossing over showed that uvs was linked to LFY3 which was on chromosome 5.

• Animal Systematics, Evolution and Diversity
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• v.36 no.4
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• pp.347-353
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• 2020

Although sea slaters Ligia have a significant role in rocky shore habitats, their taxonomic entities have not been clearly understood. In this study, we investigated whether genetic variation inferred from a nuclear genetic marker, namely amplified fragment length polymorphism (AFLP), would conform to that of a mitochondrial DNA marker. Using both the mitochondrial DNA marker and the AFLP marker amplified by the six selective primer sets, we analyzed 95 Ligia individuals from eight locations from East Asia. The direct sequencing of mitochondrial 16S rRNA gene revealed three distinct genetic lineages, with 9.8-11.7 Kimura 2-parameter genetic distance. However, the results of AFLP genotyping analysis with 691 loci did not support those of mitochondrial DNA, and revealed an unexpectedly high proportion of shared polymorphisms among lineages. The inconsistency between the two different genetic markers may be explained by difference in DNA evolutionary history, for example inheritance patterns, effective population size, and mutation rate. The other factor is a possible genomic island of speciation, in that most of the genomic parts are shared among lineages, and only a few genomic regions have diverged.