• Journal of Life Science
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• v.21 no.9
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• pp.1301-1309
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• 2011

The major function of adipocytes is to store fat in the form of triglycerides. One of the signaling pathways known to affect adipogenesis, i.e. fat formation, is the WNT/${\beta}$-catenin pathway which inhibits the expression and activity of key regulators of adipogenesis. The purpose of this research is to find genes among the WNT/${\beta}$-catenin pathway which regulate adipogenesis by using small interfering (si) RNA and to find the association of single nucleotide polymorphisms (SNPs) of the gene with serum triglyceride levels in the human population. To elucidate the effects of ${\beta}$-catenin siRNA on adipogenesis key factors, PPAR${\gamma}$ and C/EBP${\alpha}$, we performed real-time PCR and western blotting experiments for the analyses of mRNA and protein levels. It was found that the siRNA-mediated knockdown of ${\beta}$-catenin upregulates adipogenesis key factors. However, upstream regulators of the WNT/${\beta}$-catenin pathway, such as DVL2 and LRP6, had no significant effects compared to ${\beta}$-catenin. These results indicate that ${\beta}$-catenin is a candidate gene for human fat accumulation. In general, serum triglyceride level is a good indicator of fat accumulation in humans. According to statistical analyses of the association between serum triglyceride level and SNPs of ${\beta}$-catenin, -10,288 C>T SNP (rs7630377) in the promoter region was significantly associated with serum triglyceride levels (p<0.05) in 290 Korean subjects. On the other hand, serum cholesterol levels were not significantly associated with SNPs of the ${\beta}$-catenin gene. The results of this study showed that ${\beta}$-catenin is associated with fat accumulation both in vitro and in the human population.

• Korean Journal of Breeding Science
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• v.42 no.4
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• pp.397-406
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• 2010

Field screening method has been commonly used for purity test of $F_1$ hybrid seeds in melon and oriental melon. However, as this method takes a lot of time and cost, molecular marker-based purity test is necessary. To develop molecular markers for purity test, thirty pairs of SNP (single nucleotide polymorphism) primers were obtained from melon EST sequences, and 10 polymorphic markers showing HRM (high resolution melting) polymorphisms between parents of two melon cultivars and one oriental melon cultivar were selected. Blind tests were performed to validate usefulness of the selected markers for purity test. Blind test results showed that HRM genotypes were matched with the expected identity of individual sample, $F_1$ hybrid, male or female parents. Three HRM-based SNP markers were converted to CAPS markers for general use which is favor to breeders. We expect that SNP markers developed in this study will be useful for purity test of $F_1$ hybrid seeds in melon and oriental melon.

• Journal of Plant Biotechnology
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• v.46 no.3
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• pp.165-171
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• 2019

Marker-assisted backcrossing (MABC) is useful for selecting an offspring with a highly recovered genetic background for a recurrent parent at early generation to various crops. Moreover, marker-assisted backcrossing (MABC) along with marker-assisted selection (MAS) contributes immensely to overcome the main limitation of the conventional breeding and it accelerates recurrent parent genome (RPG) recovery. In this study, we were employed to incorporate rin gene(s) from the donor parent T13-1084, into the genetic background of HK13-1151, a popular high-yielding tomato elite inbred line that is a pink color fruit, in order to develop a rin HK13-1084 improved line. The recurrent parent genome recovery was analyzed in early generations of backcrossing using SNP markers obtained from genotyping-by-sequencing analysis. From the $BC_1F_1$ and $BC_2F_1$ plants, 3,086 and 4868 polymorphic SNP markers were obtained via GBS analysis, respectively. These markers were present in all twelve chromosomes. The background analysis revealed that the extent of RPG recovery ranged from 56.7% to 84.5% and from 87.8% to 97.8% in $BC_1F_1$ and $BC_2F_1$ generations, respectively. In this study, No 5-1 with 97.8% RPG recovery rate among $BC_2F_1$ plants was similar to HK13-1151 strain in the fruit shape. Therefore, the selected plants were fixed in $BC_2F_2$ generation through selfing. MAS allowed identification of the plants that are more similar to the recurrent parent for the loci evaluated in the backcross generations. MABC can greatly reduce breeding time as compared to the conventional backcross breeding. For instance, MABC approach greatly shortened breeding time in tomato.

• Journal of Life Science
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• v.29 no.1
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• pp.1-8
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• 2019

In Hanwoo cattle (Korean native cattle), there is a scarcity of comparative analysis papers using highdepth sequencing and haplotype phasing, particularly a comparative analysis of the Truseq Synthetic Long-Read Haplotyping sequencing platform serviced by Illumina (TSLRH) versus the Chromium Genome Sequencing platform serviced by 10X Genomics (10XG). DNA was extracted from the sperm of a Hanwoo breeding bull (ID: TN1505D2184/27214) provided by Hanwoo research canter and used for the generation of sequence data from both the sequencing platforms. We then identified SNVs using an appropriate analysis pipeline tailored for each platform. The TSLRH and 10XG platforms generated a total of 355,208,304 and 1,632,772,004 reads, respectively, corresponding to a Q30 (%) of 89.04% and 88.60%, respectively, of which 351,992,768(99.09%) and 1,526,641,824(93.50%) were successfully mapped. For the TSLRH and 10XG platforms, the mean depth of the sequencing was 13.04X and 74.3X, the longest phase block was 1,982,706 bp and 1,480,081 bp, the N50 phase block was 57,637 bp and 114,394 bp, the total number of SNVs identified was 4,534,989 and 8,496,813, and the total phased rate was 72.29% and 87.67%, respectively. Moreover, for each chromosome, we identified unique and common SNVs using both sequencing platforms. The number of SNVs was directly proportional to the length of the chromosome. Based on our results, we recommend the use of the 10XG platform for haplotype phasing and SNV identification, as it generated a longer N50 phase block, in addition to a higher mean depth, total number of reads, total number of SNVs, and phase rate, than the TSLRH platform.

• Journal of the Korean Society of International Agriculture
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• v.30 no.4
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• pp.277-284
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• 2018

Meat quality has always been one of the most important factors that controls the choice of pork consumers and is of great interest in the pig industry. In this study, we identified a single nucleotide polymorphism (SNP) in the enoyl-CoA delta isomerase 2 (ECI2) gene in Berkshire pigs (n = 430) by analyzed the association between the SNP and meat quality traits. The non-synonymous SNP in the ECI2 gene is located at c.608 C > G and resulted in an amino acid change from threonine to serine. Significant associations between the SNP and meat quality traits, such as redness (CIE a), and the $pH_{24hr}$, were revealed in both the dominant and co-dominant models, whereas carcass weight, drip loss, and fat content and moisture content were significantly associated only with the dominant model. In barrow, the SNP was significantly associated with CIE a, drip loss, and $pH_{24hr}$, whereas in gilt, only a significant relationship with moisture content was observed. GG genotype pigs had a higher $pH_{24hr}$ and lower drip loss. Because $pH_{24hr}$ and drip loss are considered the most important meat quality traits, GG genotype pork is high-quality meat compared to that from other genotypes. In conclusion, the SNP in the ECI2 gene is significantly associated with several meat quality traits. These traits and could be as genetic markers in molecular breeding programs for improving meat quality.

• Journal of Life Science
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• v.32 no.1
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• pp.29-35
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• 2022

This study was conducted to analyze the genetic polymorphisms of dopamine receptor D4 (DRD4) in horse breeds and its association with substrate characteristics in Jeju crossbreds (Jeju Horse × Thoroughbred). Polymorphisms in DRD4 are candidate genes associated with temperament in various mammals, including humans. Single nucleotide polymorphism (SNP) G292A in the exon 3 region of the horse DRD4 has a reported association with curiosity and vigilance in thoroughbreds. Sanger sequencing was used to identify polymorphisms of the mutations in DRD4 in three horse breeds. The SNP frequency in Jeju horses was significantly different from the frequency in other breeds. Character evaluation, conducted in the Jeju crossbreds and scored using a temperament test and contact test, revealed a high correlation between each test. Comparison of the polymorphism in the DRD4 of horses and the results of the character evaluation revealed lower scores for all temperaments in horses carrying allele A. Comparison of the SNP of G292A and blood dopamine levels in Jeju crossbreds showed 2.87 times higher levels for the GA type than for the GG type. This study identified an association between DRD4 polymorphism and various test methods for evaluating horse temperament and levels of neurotransmitters. Further research could validate the use of this gene as a genetic marker for character evaluation.

• The Journal of Internal Korean Medicine
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• v.43 no.6
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• pp.1105-1121
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• 2022

Objectives: The purpose of this study is to explore the effectiveness and safety of frequently used clinical herbal medicines (Yijung-tang [Lizhong-tang, LJT], Pyeongwi-san [Pingwei-san, PWS], and Shihosogan-tang [Chaihu Shugan-tang, SST]) in patients with functional dyspepsia (FD) when administered according to herbal medicine and Korean medicine pattern identification. The results of this study will be used to standardize the diagnostic instrument used in Korean medicine and to investigate biomarkers of Korean medicine pattern identification. Methods: This study will be a randomized, assessor-blind, 3-arm, parallel, open-label, multi-center clinical trial. A total of 300 FD participants will be recruited from 3 Korean medical hospitals and assigned to the LJT (n=100), PWS (n=100), and SST (n=100) groups according to FD pattern identification. The patients will take the medication for 8 weeks, 3 times a day, before or between meals. The primary outcome will be total dyspepsia symptom (TDS) and the secondary outcomes will be adequate relief (AR) for dyspepsia, overall treatment effect (OTE), visual analogue scale (VAS), functional dyspepsia-related quality of life (FD-QoL), gastrointestinal symptom score (GIS), and pattern identification questionnaires. For the exploratory outcomes, we will analyze blood and fecal metabolome profiles, microbiota from fecal and saliva samples, single nucleotide polymorphism (SNP), and results of Korean medicine diagnosis device measurements (heart rate variability, and tongue, pulse, and abdominal diagnosis). Conclusions: The results of this study will prove objectivity for Korean medicine pattern identifications, and the effectiveness and safety of herbal medicines for the population with FD.

• Research in Plant Disease
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• v.29 no.3
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• pp.276-285
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• 2023

This work investigated the viral infection in jujube plants in Korea. A total of 61 samples with the symptoms of putative viral infection were collected from experimental fields and orchards. Thereafter, the samples were subjected to metatranscriptome analysis, Reverse transcription polymerase chain reaction analysis, and nucleotide sequence analysis. These analyses identified the presence of two DNA viruses, jujube-associated badnavirus (JuBV), jujube mosaic-associated virus (JuMaV), and one RNA virus, jujube yellow mottle-associated virus (JYMaV). All samples collected were confirmed to be infected by at least one of the three viruses, with most showed multiple infections. The detection rates of JuBV, JYMaV, and JuMaV were 100%, 90.2%, and 8.2%, respectively. Only three combinations of viral infections were found: 9.8% of samples showed single infection of JuBV, 82.0% showed double infection of JuBV+JYMaV, and 8.2% showed triple infection of JuBV+JYMaV+JuMaV. Sequence analysis of the three viruses showed very high homology with respective virus isolates reported in China. This study is predicted to provide fundamental data to produce virus-free jujube seedlings and represents the first report of JuBV and JuMaV infection in Korea.

• Journal of Korean Society of Forest Science
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• v.112 no.1
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• pp.40-56
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• 2023

Tree species within the Populus genus grow rapidly and have an excellent capacity to absorb carbon, conferring substantial ability to effective purify the environment. Poplar breeding can be achieved rapidly and efficiently if a genetic linkage map is constructed and quantitative trait loci (QTLs) are identified. Here, a high-density genetic linkage map was constructed for the control pollinated progeny using the genotyping-by-sequencing (GBS) technique, which is a next-generation sequencing method. A search was also performed for the genes associated with quantitative traits located in the genetic linkage map by examining the variables of height and diameter at root collar, and resilience to insect damage. The height and diameter at root collar were measured directly, while the ability to recover from insect damage was scored in a 4-year-old breeding population of aspen hybrids (Odae19 × Bonghyeon4 F1) established in the research forest of Seoul National University. After DNA extraction, paternity was confirmed using five microsatellite markers, and only the individuals for which paternity was confirmed were used for the analysis. The DNA was cut using restriction enzymes and the obtained DNA fragments were prepared using a GBS library and sequenced. The analyzed results were sorted using Populus trichocarpa as a reference genome. Overall, 58,040 aligned single-nucleotide polymorphism (SNP) markers were identified, 17,755 of which were used for mapping genetic linkages. The genetic linkage map was divided into 19 linkage groups, with a total length of 2,129.54 cM. The analysis failed to identify any growth-related QTLs, but a gene assumed to be related to recovery from insect damage was identified on linkage group (chromosome) 4 through genome-wide association study.

• Korean Journal of Plant Resources
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• v.36 no.4
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• pp.369-380
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• 2023

Developing and breeding improved legume-based food resources require collecting useful genetic traits with heritability even though requiring some time-consuming, costly, and labor intensive. We attempted to infer heritability of nine genetic traits-days to flowering, days to maturity, period from flowering to maturity, the number of seeds per pod, 100-seeds weight, and four contents such as crude protein, crude oil, crude fiber, and dietary fiber-using 455 homologous chloroplast gene sets of six species of legumes. Correlation analysis between genetic trait differences and phylogenetic distance of homologous gene sets revealed that days to flowering, the number of seeds per pod, and crude oil content were influenced by genetic factors rather than environmental factors by 62.86%, 69.45%, 57.14% of correlated genes (P-value ≤ 0.05) and days to maturity showed intermediate genetic effects by 62.42% (P-value ≤ 0.1). The period from flowering to maturity and 100-seeds weight showed different results compared to those of some previous studies, which may be attributed to highly complicated internal (epistatic or additive gene effects) and external effects (cultural environment and human behaviors). Despite being slightly unexpected, our results and method can widely contribute to analyze heritability by including genetic information on mitochondria, nuclear genome, and single nucleotide polymorphisms.