• Journal of Veterinary Clinics
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• v.36 no.4
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• pp.190-195
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• 2019

We aimed to identify genomic variations as well as the marker genes related with chronic mitral valve disease (CMVD) in Canis lupus familiaris using whole genome resequencing, which provides valuable resources for further study. Two ten-year old female Canis lupus familiaris English cocker spaniels were used for this study, one control and one who had been diagnosed as CMVD. For the whole genome resequencing, muscles from the left ventricular wall were collected from each dog. With the HiSeq DNA Shotgun library and $HiSeq^{TM}$ 2000 platform, whole genome resequencing was performed. From the results, we identified 5 million and 6 million variants in gene expression in the control and CMVD-diagnosed subject, respectively. We then selected the top 1,000 genes from the SNP, INS, and DEL mutation and 675 genes among them were overlapped for every mutation between the control and CMVD-diagnosed patient. Interestingly, in both groups, the intron variant (91.16 and 91.18%) and upstream variant (3.10 and 3.08%) are most highly related. Among the overlapped 675 genes, gene ontology for intracellular signal transduction is highly counted in INS, and DEL, and SNPs (35, 33, 31, respectively). In this study, we found that the COL and CDH gene families could be key molecules in identifying the difference in gene expression between control and CMVD-diagnosed dogs. We believe further studies will prove the importance of variants in key molecule expression and that these data will serve as a valuable foundation stone the study of canine CMVD.

• Genomics & Informatics
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• v.20 no.2
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• pp.19.1-19.15
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• 2022

Alfalfa (Medicago sativa) is an important food and feed crop which rich in mineral sources. The WUSCHEL-related homeobox (WOX) gene family plays important roles in plant development and identification of putative gene families, their structure, and potential functions is a primary step for not only understanding the genetic mechanisms behind various biological process but also for genetic improvement. A variety of computational tools, including MAFFT, HMMER, hidden Markov models, Pfam, SMART, MEGA, ProtTest, BLASTn, and BRAD, among others, were used. We identified 34 MsWOX genes based on a systematic analysis of the alfalfa plant genome spread in eight chromosomes. This is an expansion of the gene family which we attribute to observed chromosomal duplications. Sequence alignment analysis revealed 61 conserved proteins containing a homeodomain. Phylogenetic study sung reveal five evolutionary clades with 15 motif distributions. Gene structure analysis reveals various exon, intron, and untranslated structures which are consistent in genes from similar clades. Functional analysis prediction of promoter regions reveals various transcription binding sites containing key growth, development, and stress-responsive transcription factor families such as MYB, ERF, AP2, and NAC which are spread across the genes. Most of the genes are predicted to be in the nucleus. Also, there are duplication events in some genes which explain the expansion of the family. The present research provides a clue on the potential roles of MsWOX family genes that will be useful for further understanding their functional roles in alfalfa plants.

• Journal of Species Research
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• v.11 no.4
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• pp.266-277
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• 2022

The current surveys of Ulva in the subtidal area around Jeju Island give a chance to discover unrecorded green algal species of the Korean macroalgal flora. As a result of this investigation, we found Ulva adhaerens Matusmoto & Shimada, inhabiting the subtidal regions, up to 15 m deep, and conducted the DNA barcoding on plastid rbcL-3P and tufA regions with describing the morphological characteristics. Our specimens of U. adhaerens forms a monophyletic clade with the Japanese type specimen and U. piritoka Ngāti Kuri, Heesch & W.A. Nelson from New Zealand exhibiting each 0.3% sequence divergences, respectively, in the plastid rbcL-3P. The genetic variation of U. adhaerens clade is 1.0-3.9% in rbcL-3P and 4.8-9.8% in tufA to each Ulva species, including the generic type, U. lactuca Linneaus. The morphology of Korean U. adhaerens specimens is identical to the type specimens of U. adhaerens from Japan having the development of rhizoidal filaments from both of the cell layers of the distromatic blade and the extension of rhizoidal clumps with adhesive trait between blades by extended rhizoidal clumps at the basal blades. The thallus attachment to substrate is by numerous minute discoidal plates made up of rhizoids originating from the inner part of distromatic blades in basal. Although there are still some problems to resolve the relationship between U. adhaerens and U. piritoka in the rbcL dataset and the phylogenetic pattern of the Group II intron of rbcL, we propose the new record of U. adhaerens in Korean macroalgal flora based on the morphological characteristics of Korean specimens. Continued study of the genus Ulva by morphological and molecular assessment will delimit the species of Ulva, elucidate the relationships between them, and uncover the species diversity.

• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.277-277
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• 2022

Lignin modification has been a breeding target for the improvements of forage digestibility and fermentation in whole crop silage(WCS) rice. In rice, gold hull and internode 2 (gh2) was identified as a lignin-deficient mutant. gh2 exhibits a reddish-brown pigmentation in the hull and the internode is located on the short arm of chromosome 2 and codes for cinnamyl-alcohol dehydrogenase (CAD). To develop WCS rice variety improved digestibility and fermentation, we measured acid detergent fiber (ADF), lignin and total digestible nutrient (TDN) calculated from ADF (TDN=88.9-(0.79% × ADF) and performed marker-assisted selection using CAD(Os2g0187800) gene first intron region specific marker with 55 Jungmo1038/J.collection lines. Those lines had lignin content range from 0.82 to 6.61%, ADF from 15.8 to 45.8%, TDN from 52.7 to 78.8 compared to 'Jungmo1038'(1.53,20.7,72.6), 'J.collection'(0.98,12.8,78.8%) and gh2 were introgressed into 44 lines. Considering on these genotype and low-lignin phenotype, we finally selected 2 elite lines(Suweon668, Suweon669). Suweon668 and Suweon669 line are high biomass-low lignin lines that the ADF content is relatively low, even though the dry matter weight is high. Also they have lodging and shattering resistance and glabrous leaf and hull important to improve cattle palatability. Our results will provide that rice can be improved for forage digestibility and fermentation with low lignin concentration.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.16 no.2
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• pp.109-114
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• 2016

Carbamoyl phosphate synthetase 1 (CPS1) deficiency is an autosomal recessive urea cycle disorder which causes hyperammonemia. CPS1 is the first enzyme step in the urea cycle and almost patients present their symptoms during neonatal period. We report a case of CPS1 deficiency in a boy who developed symptoms including lethargy and seizure at 3 days of age. The ammonia level was up to $2,325{\mu}mol/L$, sodium benzoate (250 mg/kg/d) and high calories of both dextrose and lipid was promptly administered. Central access by experienced pediatric surgeon and emergent continuous hemodialysis by pediatric nephrologist was performed within 3 hours and ammonia was less than $100{\mu}mol/L$ at 5 days of age. Currently, he has showed excellent response to treatments including scavenging drugs and a low-protein diet. Despite of diffuse increasing signal intensity on cerebral white matters and basal ganglia on brain MRI, his development and weight gain were good at the last follow-up at 11 months of age. Molecular assay of the CPS1 gene demonstrated that patient had compound heterozygous for c.1529del ($p.Gly510Alafs^*5$) in exon 14 and c.3142-1G>C (IVS25(-1)G>C) in intron 25 and exon 26 boundary. The splicing mutation was novel mutation and inherited from patient's mother. Here, we report a neonatal lethal type CPS1 deficiency patient having novel mutation.

• Journal of Animal Science and Technology
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• v.51 no.1
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• pp.9-14
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• 2009

Insulin-like growth factor 2 (IGF2) is the first identified imprinted gene, which is paternally expressed in multiple mammalian species. A paternally expressed QTL for muscle growth and backfat thickness (BFT) has previously been identified near the IGF2 locus on the distal tip of pig chromosome 2 (SSC2p). Therefore the IGF2 gene is considered an economically important candidate gene for pig industry. Herein, this study explored genetic variation of IGF2 for in3-G3072A, in7-G162C and a new SNP in intron7 (C1589T) in Korean native pig (KNP) and commercial pig breeds, and detected their linkage disequilibrium within these breeds. Furthermore we investigated the effect of in3-G3072A on IGF2 gene expression in post-natal muscle and backfat tissues. The real-time quantitative PCR results showed that animals inherited allele G from a KNP sire had significant higher IGF2 gene expression in backfat tissue than those inherited allele A from a Yorkshire sire, however opposite situation in muscle. These results demonstrated the allele 3072G is associated with a higher IGF2 gene expression in fat tissues, but low gene expression in muscle tissues when compared with the 3072A allele. These results suggest that KNP with lower muscle mass and higher fat deposition might be associated with a higher frequency of the 3072G allele, and selecting KNP based on IGF2 genotypes could result in an economic benefit to KNP producers.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.7
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• pp.2929-2937
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• 2015

Endothelial nitric oxide synthase (eNOS or NOS3) produces nitric oxide and genetic polymorphisms of NOS3 gene play significant roles in various processes of carcinogenesis. The results from published studies on the association between NOS3 G894T and NOS3 intron 4 (4a/b) polymorphisms and cancer risk are conflicting and inconclusive. However, i n order to assess this relationship more precisely, a meta-analysis was performed with PubMed (Medline), EMBASE and Google web searches until February 2014 to select all published case-control and cohort studies. Genotype distribution data were collected to calculate the pooled odd ratios (ORs) and 95% confidence intervals (CIs) to evaluate the strength of association. A total of 10,546 cancer cases and 10,550 controls were included from twenty four case-control studies for the NOS3 G894T polymorphism. The results indicated no significant association with cancer risk as observed in allelic (T vs G: OR=1.024, 95%CI=0.954 to 1.099, p=0.508), homozygous (TT vs GG: OR=1.137, 95%CI=0.944 to 1.370, p=0.176), heterozygous (GT vs GG: OR=0.993, 95%CI=0.932 to 1.059, p=0.835), recessive (TT vs GG+GT: OR=1.100, 95%CI=0.936 to 1.293, p=0.249) and dominant (TT+GT vs GG: OR=1.012, 95%CI=0.927 to 1.105, p=0.789) genetic models. Similarly, a total of 3,449 cancer cases and 3,691 controls were recruited from fourteen case-control studies for NOS3 4a/b polymorphism. Pooled results indicated no significant association under allelic (A vs B: OR=0.981, 95%CI=0.725 to 1.329, p=0.902), homozygous (AA vs BB: OR=1.166, 95%CI=0.524 to 2.593, p=0.707), heterozygous (BA vs BB: OR=1.129, 95%CI=0.896 to 1.422, p=0.305), dominant (AA+BA vs BB: OR=1.046, 95%CI=0.779 to 1.405, p=0.763) and recessive (AA vs BB+BA: OR=1.196, 95%CI=0.587 to 2.439, p=0.622) genetic contrast models. This meta-analysis suggests that G894T and 4a/b polymorphisms of NOS3 gene are not associated with increased or decreased risk of overall cancer.

• Journal of Animal Science and Technology
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• v.51 no.4
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• pp.289-294
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• 2009

Inositol 1,4,5-triphosphate receptor type 1 (IP3R1) is a $Ca^{2+}$ release channel that responds to the second messenger IP3 and that modulates diverse cellular functions such as contraction/excitation, secretion, gene expression and cellular growth. We discovered single nucleotide polymorphisms (SNPs) within IP3R1 gene and analyzed associations between gene polymorphisms and carcass traits in Korean cattle (Hanwoo) in order to develop novel DNA markers at genomic level. Three SNPs were detected at the position of g.1428617A>G, g.1418843C>T and g.1414377C>T with 24 unrelated Hanwoo samples by direct sequencing of the PCR products. We found that genotype of g.1414377C>T SNP was associated with live weight (P<0.05) and carcass weight (P<0.01) using the general linear model of SAS package. These results suggest that polymorphism of IP3R1 gene was associated with weight-related traits in Hanwoo.

• Journal of Life Science
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• v.27 no.7
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• pp.760-766
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• 2017

Genotypes of the nucleotide substitution g.23655332G>C of SNP marker rs385360448 at Lysophospholipase I (LYPLA1) gene intron 7, were tested for their effect on the carcass traits of Hanwoo and Jeju Crossbred cattle ($F_1$ progeny produced between Hanwoo ${\times}$ Jeju Black cattle) populations on Jeju Island. In the Hanwoo steer population, the meats containing LYPLA1 rs385360448 G/- genotypes showed significantly higher marbling scores and greater texture indices, compared to those of rs385360448 C/C homozygous animals (p<0.05). However, the LYPLA1 genotypes were not associated with the levels of carcass weight, backfat thickness, eye muscle area (EMA), meat color, and fat color (p>0.05). On the other hand, in the JCC steer population, the LYPLA1 G/- harboring meats showed significantly greater EMA levels, compared to those of C/C homozygotes (p<0.05). The results of the present study indicate that the LYPLA1 genotypes could alter the levels of intramuscular fat deposition, texture index, and eye muscle area via phospholipid metabolism in the Longissimus dorsi muscle of the cattle. These findings suggested that LYPLA1 genotypes may effect molecular genetic markers in the improvement of carcass traits of Hanwoo and Jeju Black industrial cattle populations on Jeju Island.

• Journal of Periodontal and Implant Science
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• v.34 no.3
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• pp.607-622
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• 2004

Recently epidemiologic studies have indicated that the patients with periodontitis may have increased risk of ischemic cardiovascular events, and have suggested the important roles of blood cytokines and acute reactant proteins in the systemic infection and inflammatory response. Periodontitis and coronary heart disease (CHD) may share the common risk factors and the genetic mechanism associated with interleukin(IL)-1A, B and RA genotype may be involved in the production of IL-1. This study was aimed to investigate the relationship between angiographically defined CHD and periodontitis as chronic Gram-negative bacterial infection and to determine whether the IL-1 gene polymorphism is associated in both diseases. Patients under the age of 60 who had undergone diagnostic coronary angiography were enrolled in this study. Subjects were classified as positive CHD (+CHD, n=37) with coronary artery stenosis more than 50% in at least one of major epicardial arteries, and negative CHD (-CHD, n=30) without significant stenosis. After recording the number of missing teeth, periodontal disease severity was measured by means of plaque index (PI), gingival index (GI), bleeding on probing (BOP), probing depth (PD), clinical attachment level (CAL), and radiographic bone loss around all remaining teeth. Gingival crevicular fluid (GCF) was collected from the 4 deepest periodontal pockets and assessed for cytokine ($IL-1{\beta}$, IL-6, IL-1ra, tumor necrosis $factor-{\alpha}$, and prostaglandin $E_2$). Additionally, blood CHD markers, lipid profile, and blood cytokines were analyzed. IL-1 gene cluster genotyping was performed by polymerase chain reaction and enzyme restriction using genomic DNA from buccal swab, and allele 2 frequencies of IL-1A(+4845), IL-1B(+3954), IL-B(-511), and IL-1RA(intron 2) were compared between groups. Even though there was no significant difference in the periodontal parameters between 2 groups, GCF level of $PGE_2$ was significantly higher in the +CHD group(p<0.05). Correlation analysis showed the positive relationship among PD, CAL and coronary artery stenosis(%) and blood $PGE_2$. There was also significant positive relationship between the periodontal parameters (PI, PD, CAL) and the blood CHD markers (leukocyte count, C-reactive protein, and lactic dehyrogenase). IL-1 gene genotyping showed that IL-1A(+3954) allele 2 frequency was significantly higher in the +CHD group compared with the -CHD group (15% vs. 3.3%, OR 5.118,p=0.043). These results suggested that periodontal inflammation is related to systemic blood cytokine and CHD markers, and contributes to cardiovascular disease via systemic inflammatory reaction. IL-1 gene polymorphism might have an influence on periodontal and coronary heart diseases in Korean patients.