• Journal of Life Science
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• v.25 no.3
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• pp.349-356
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• 2015

Thanks to recent advances in next-generation sequencing (NGS) technology, diverse livestock species have been dissected at the genome-wide sequence level. As for cattle, there are currently four Korean indigenous breeds registered with the Domestic Animal Diversity Information System of the Food and Agricultural Organization of the United Nations: Hanwoo, Chikso, Heugu, and Jeju Heugu. These native genetic resources were recently whole-genome resequenced using various NGS technologies, providing enormous single nucleotide polymorphism information across the genomes. The NGS application further provided biological such that Korean native cattle are genetically distant from some cattle breeds of European origins. In addition, the NGS technology was successfully applied to detect structural variations, particularly copy number variations that were usually difficult to identify at the genome-wide level with reasonable accuracy. Despite the success, those recent studies also showed an inherent limitation in sequencing only a representative individual of each breed. To elucidate the biological implications of the sequenced data, further confirmatory studies should be followed by sequencing or validating the population of each breed. Because NGS sequencing prices have consistently dropped, various population genomic theories can now be applied to the sequencing data obtained from the population of each breed of interest. There are still few such population studies available for the Korean native cattle breeds, but this situation will soon be improved with the recent initiative for NGS sequencing of diverse native livestock resources, including the Korean native cattle breeds.

• 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 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.

• 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.

• 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.

• Journal of Animal Science and Technology
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• v.54 no.1
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• pp.1-8
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• 2012

This study aimed to investigate the single nucleotide polymorphisms (SNPs) of the porcine MC4R gene and validate the effect of the MC4R genotype for marker assisted selection (MAS). Six amplicons were produced to analyze the entire base sequences of the porcine MC4R gene and six SNPs were detected (c.-780C>G, c.-135C>T, c.175C>T-Leu59Leu, c.707A>G-Arg236His, c.892A>G-Asp298Asn, and c.*430A>T). Linkage disequilibrium (LD) of the six SNPs was analyzed by performing haploid analysis. There was a perfect linkage disequilibrium in c.-780C>G, c.-135C>T, c.175C>T-Leu59Leu, c.707A>G-Arg236His, and c.*430A>T. Only the c.892A>G (Asp298Asn) SNP showed a very low LD with an $r^2$ value of 0.028 and the D' value of 0.348. As a result, the two SNPs-c.707A>G (Arg236His) and c.892A>G (Asp298Asn)-were selected to extract the genotype frequencies from the 5 pig breeds by using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) genotype analysis method. The SNP frequency of c.707A>G (Arg236His) indicated the presence of the A (His) allele only in Yorkshire, while the G allele was fixed in the KNP, Landrace, Berkshire, and Duroc. Association analysis was carried out in 484 pigs with the c.707A>G (Arg236His) SNP and the meat quality traits of four different pig cross populations: a significant association was noted in crude fat, sirloin moisture, meat color, and the degree of red and yellow coloration. The frequency of the c.892A>G(Asp298Asn) SNP genotype varied among the breeds; while Duroc showed the highest frequency of the A (Asn) allele, KNP showed the highest frequency of the G (Asp) allele. Association analysis was carried out in 1126 pigs with the c.892A>G (Asp298Asn) SNP and the meat quality traits of four pig populations: a highly significant linkage was noted in the back-fat thickness (P<0.002). It was found that the back-fat thickness was higher in individuals with the AA genotype than in those with the AG or GG genotype. Thus, in this study, we verified that the c.892A>G (Asp298Asn) SNP in the pig MC4R gene has a sufficient effect as a gene marker for MAS in Korean pork industry.