• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.259-259
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• 2022

Soil salinity is a major factor that reduces crop yields. The amount of soil affected by salinity is about 83 million hectares (FAO 2000), which is increasing due to the effects of climate change. In soybean [Glycine max (L.) Merr.], nutritional properties such as protein, starch, and sucrose content together with biomass and yield tends to reduce due to excessive salt. As a result of QTL mapping using the 169 F_2:3 population from the KA-1285 (salt-tolerant) × Daepung (salt-sensitive) in a previous study, two major QTLs (Gm03_39796778 and Gm03_40600088) related to salt tolerance were found on chromosome 3. In this study, the CDS region of the Gmsalt3 gene was analyzed using the ABI 3730x1 DNA Analyzer (Macrogen, Korea). The sequence of Gmsalt3 gene in KA-1285 was compared with Williams 82.a4.vl and PI483463 (Glycine soja). Two transversions were found at exon6 in KA-1285 and PI483463. Currently, whole genome sequencing and variation analysis using the Illumine Novaseq 6000 machine (Illumina, USA) are in progress. The results of this study can provide useful molecular markers for the selection of salt-tolerant soybeans and can be used as basic data for future salt-tolerant gene research.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2022년도 추계학술대회
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• pp.261-261
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• 2022

Cowpea [Vigna unguiculata (L.) Walp] is one of the most important grain legumes that enhance soil fertility and is well-adapted to various abiotic stress. Also, it is cultivated worldwide as a tropical annual crop, and the semi-arid regions are known as the main cowpea-produced regions. However, accumulation of soil salinity induced by low rainfall in these regions is reducing crop yields and quality. In general, plants exposed to soil salinity cause an accumulation of high ion chloride, which leads to the degradation of root and leaf proteins. In this study, we identified candidate genes associated with salinity tolerance through an analysis of differentially expressed genes (DEGs) in four cowpea germplasms with contrasting salinity tolerance. A total of 553,776,035 short reads were obtained using the Illumina Novaseq 6000 platform for RNA-Seq, which were subsequently aligned to the reference genome of cowpea Vunguiculata v1.2. A total of9,806 DEGs were identified between NaCl treatment and control of four cowpea germplasms. Among these DEGs, functions related to salt stress such as calcium transporter and cytochrome-450 family were associated with salt stress. In GO analysis and KEGG analysis, these DEGs were enriched in terms such as the "phosphorylation", ''extracellular region", and "ion binding". These RNA-seq results will improve the understanding of the salt tolerance of cowpea and can be used as useful basic data for molecular breeding technology in the future.

• Anatomy and Cell Biology
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• 제56권1호
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• pp.86-93
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• 2023

Age at death estimation has always been a crucial yet challenging part of identification process in forensic field. The use of human skeletons have long been explored using the principle of macro and micro-architecture change in correlation with increasing age. The clavicle is recommended as the best candidate for accurate age estimation because of its accessibility, time to maturation and minimal effect from weight. Our study applies pre-trained convolutional neural network in order to achieve the most accurate and cost effective age estimation model using clavicular bone. The total of 988 clavicles of Thai population with known age and sex were radiographed using Kodak 9000 Extra-oral Imaging System. The radiographs then went through preprocessing protocol which include region of interest selection and quality assessment. Additional samples were generated using generative adversarial network. The total clavicular images used in this study were 3,999 which were then separated into training and test set, and the test set were subsequently categorized into 7 age groups. GoogLeNet was modified at two layers and fine tuned the parameters. The highest validation accuracy was 89.02% but the test set achieved only 30% accuracy. Our results show that the use of medial clavicular radiographs has a potential in the field of age at death estimation, thus, further study is recommended.

• Biomolecules & Therapeutics
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• 제32권2호
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• pp.214-223
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• 2024

Metabolic abnormalities in the liver are closely associated with diverse metabolic diseases such as non-alcoholic fatty liver disease, type 2 diabetes, and obesity. The aim of this study was to evaluate the ameliorating effect of robinetin (RBN) on the significant pathogenic features of metabolic failure in the liver and to identify the underlying molecular mechanism. RBN significantly decreased triglyceride (TG) accumulation by downregulating lipogenesis-related transcription factors in AML-12 murine hepatocyte cell line. In addition, mice fed with Western diet (WD) containing 0.025% or 0.05% RBN showed reduced liver mass and lipid droplet size, as well as improved plasma insulin levels and homeostatic model assessment of insulin resistance (HOMA-IR) values. CD38 was identified as a target of RBN using the BioAssay database, and its expression was increased in OPA-treated AML-12 cells and liver tissues of WD-fed mice. Furthermore, RBN elicited these effects through its anti-histone acetyltransferase (HAT) activity. Computational simulation revealed that RBN can dock into the HAT domain pocket of p300, a histone acetyltransferase, which leads to the abrogation of its catalytic activity. Additionally, knock-down of p300 using siRNA reduced CD38 expression. The chromatin immunoprecipitation (ChIP) assay showed that p300 occupancy on the promoter region of CD38 was significantly decreased, and H3K9 acetylation levels were diminished in lipid-accumulated AML-12 cells treated with RBN. RBN improves the pathogenic features of metabolic failure by suppressing the p300-CD38 axis through its anti-HAT activity, which suggests that RBN can be used as a new phytoceutical candidate for preventing or improving this condition.

• Animal Bioscience
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• 제37권3호
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• pp.461-470
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• 2024

Objective: The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits. Methods: To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (pi, F_st, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions. Results: The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (pi, F_st, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (PLAG1), dedicator of cytokinesis 3 (DOCK3), ephrin A2 (EFNA2), DAZ associated protein 1 (DAZAP1), Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), mediator complex subunit 13 (MED13), and decaprenyl diphosphate synthase subunit 2 (PDSS2), most of which were enriched in pathways related to muscle growth and differentiation and immunity. Conclusion: In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle.

• 전자공학회논문지CI
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• 제43권3호
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• pp.30-38
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• 2006

본 논문에서는 스테레오 얼굴영상으로부터 3차원 정보인 거리와 깊이 정보를 이용해 거리에 따라 얼굴인식률이 떨어지는 것을 개선하였다. 단안 영상은 객체의 거리, 크기, 이동, 회전, 깊이 등의 불확실한 정보로 인해 인식률이 떨어지는 문제점이 있다. 또한 얼굴의 회전, 조명, 표정변화 등의 영상정보가 취득되지 않으면 인식률이 매우 저하되는 단점이 있다. 그래서 본 연구는 이와 같은 문제점을 해결하고자 한다. 제안된 방법은 눈 검출 알고리듬, 얼굴의 회전 방향분석, PCA(Principal Component Analysis)로 구성된다. 또한 제한된 영역에서 얼굴을 고속으로 검출하기 위해 RGB컬러공간에서 YCbCr공간으로 변환한다. 얼굴후보 영역에서 다층 상대적인 밝기 맵을 생성하여 얼굴의 기하학적인 구조로부터 얼굴인지를 판별한다. 스테레오 얼굴영상으로부터 거리 및 눈과 입의 깊이 정보를 취득하고, 거리에 따라 확대, 축소, 이동, 회전 등의 정규화를 통해 $92{\times}112$ 크기의 얼굴을 검출한다. 검출된 왼쪽 얼굴영상과 추정된 방향의 차를 PCA로 학습한다. 제안된 방법은 정면에서 최대 95.8%(100cm), 포즈변화에 따라 98.3%의 인식률을 얻을 수 있었다. 따라서 실험을 통하여 제안된 방법은 거리에 따라 확대, 축소와 회전 등의 정확한 정규화로 높은 인식률을 얻을 수 있음을 보였다.

• 한국수정란이식학회지
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• 제31권3호
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• pp.293-297
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• 2016

For evaluating the boar semen quality, sperm motility is an important parameter because the movement of sperm indicates active metabolism, membrane integrity and fertilizing capacity. Phospholipase C zeta (PLCz) is important enzyme in spermatogenesis, but the effect has not been confirmed in pigs yet. Therefore, this study was aimed to analyze their association with sperm motility and kinematic characteristics. DNA samples from 124 Duroc pigs with records of sperm motility and kinematic characteristics [total motile spermatozoa (MOT), curvilinear velocity (VCL), straight-line velocity (VSL), the ratio between VSL and VCL (LIN), amplitude of lateral head displacement (ALH)] were subjected. A SNP in non-coding region of PLCz g.158 A > C was associated with MOT (p < 0.05), VCL (p < 0.01), LIN (p < 0.01) and ALH (p < 0.05) in Duroc population. Therefore, we suggest that the intron region of the porcine PLCz gene may be used as a molecular marker for Duroc boar semen quality, although its functional effect was not defined yet. Whether the association is due to the candidate gene or not require further verification. Thus, it will be of interest to continue association studies in the regions surrounding those genes.

• BMB Reports
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• 제38권1호
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• pp.77-81
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• 2005

The monocyte chemotactic protein-3 (MCP3), on chromosome 17q11.2-q12, is a secreted chemokine, which attracts macrophages during inflammation and metastasis. In an effort to discover additional polymorphism(s) in genes whose variant(s) have been implicated in asthma, we scrutinized the genetic polymorphisms in MCP3 to evaluate it as a potential candidate gene for asthma host genetic study. By direct DNA sequencing in twenty-four individuals, we identified four sequence variants within the 3 kb full genome including 1,000bp promoter region of MCP3; one in promoter region (-420T>C), three in intron (+136C>G, +563C>T, +984G>A) respectively. The frequencies of those four SNPs were 0.020 (-420T>C), 0.038 (+136C>G), 0.080 (+563C>T), 0.035 (+984G>A), respectively, in Korean population (n = 598). Haplotypes, their frequencies and linkage disequilibrium coefficients (|D'|) between SNP pairs were estimated. The associations with the risk of asthma, skin-test reactivity and total serum IgE levels were analyzed. Using statistical analyses for association of MCP3 polymorphisms with asthma development and asthma-related phenotypes, no significant signals were detected. In conclusion, we identified four genetic polymorphisms in the important MCP3 gene, but no significant associations of MCP3 variants with asthma phenotypes were detected. MCP3 variation/haplotype information identified in this study will provide valuable information for future association studies of other allergic diseases.

• Asian-Australasian Journal of Animal Sciences
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• 제20권7호
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• pp.1023-1029
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• 2007

Inhibins participate in the regulation of pituitary follicle-stimulating hormone synthesis and secretion, follicular maturation and steroidogenesis in the female. Inhibin ${\beta}_A$ gene (INHBA) was studied as a candidate gene for the prolificacy of sheep. Single nucleotide polymorphisms of the entire coding region and partial 3' untranslated region of INHBA were detected by PCR-SSCP in two high fecundity breeds (Small Tail Han and Hu sheep) and six low fecundity breeds (Dorset, Texel, German Mutton Merino, South African Mutton Merino, Chinese Merino and Corriedale sheep). Only the PCR products amplified by primers 3, 4 and 5 displayed polymorphisms. For primer 3, genotype CC was only detected in Chinese Merino sheep, genotype AA was detected in the other seven sheep breeds. Genotype BB was only detected in Hu sheep. Only Hu sheep displayed polymorphism. Eight or four nucleotide mutations were revealed between BB or CC and AA, respectively, and these mutations did not result in any amino acid change. For primer 4, genotypes EE, EG and GG were detected in Dorset and German Mutton Merino sheep, genotypes EE, EF and FF were detected in Chinese Merino sheep, only genotype EE was detected in the other five sheep breeds. Only Dorset, German Mutton Merino and Chinese Merino sheep displayed polymorphism. Sequencing revealed one nucleotide mutation ($114G{\rightarrow}A$) of exon 2 of INHBA gene between genotype FF and genotype EE, and this mutation did not cause any amino acid change. Another nucleotide change ($143C{\rightarrow}T$) was identified between genotype GG and genotype EE, and this mutation resulted in an amino acid change of $serine{\rightarrow}leucine$. For primer 5, genotypes KK and KL were detected in German Mutton Merino and Corriedale sheep, genotypes KK, LL and KL were detected in the other six sheep breeds. Genotype MM was only detected in Hu sheep. All of these eight sheep breeds displayed polymorphism. Sequencing revealed one nucleotide mutation ($218A{\rightarrow}G$) of exon 2 of the INHBA gene between genotype LL and genotype KK, and nine nucleotide mutations between genotype MM and genotype KK. These mutations did not alter amino acid sequence. The partial sequence (395 bp for exon 1 and 933 bp for exon 2) of the INHBA gene in Small Tail Han sheep (with genotype KK for primer 5) was submitted into GenBank (accession number EF192431). Small Tail Han sheep displayed polymorphisms only in the fragment amplified by primer 5. The Small Tail Han ewes with genotype LL had 0.53 (p<0.05) or 0.63 (p<0.05) more lambs than those with genotype KL or KK, respectively. The Small Tail Han ewes with genotype KL had 0.10 (p>0.05) more lambs than those with genotype KK.

• 한국응용곤충학회지
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• 제55권3호
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• pp.245-256
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• 2016

무당벌레(Harmonia axyridis)는 종내에서 초시색상패턴이 매우 다양하게 존재한다. 본 논문에서는 서로 다른 색상패턴의 무당벌레를 대상으로 amplified fragment length polymorphism (AFLP)을 실시하여 무당벌레의 초시색상 패턴간 유전형질의 차이를 확인하고자 하였다. 총 28 개의 프라이머 조합으로 실험을 실시한 결과, 총 2,741 개의 밴드가 검출되었다. 그 중 20 개의 밴드(S1-S20)만이 특정 색상패턴에서 나타났다. 이들 가운데 9 개의 밴드를 색상에 연관된 AFLP 후보 지표로 선발하였다. 밴드 가운데 S1과 S2, S20은 Succinea 1, 2 변이형에 공통적으로 나타났으며, S3와 S5는 Conspicua 변이형에 특이적이었다. 또한 S13는 Spectabilis 변이형에, S15와 S18, S19는 Succinea 2 변이형에 특이적이었다. 특정 색상패턴에만 나타나는 9 개의 AFLP 지표들은 cloning을 통해 염기서열 분석을 실시하였고, GenBank를 이용해 다른 염기 서열과 비교를 해보았지만 아무런 상동성도 찾을 수가 없었다. 무당벌레 종 내 유전적 다양성을 평가한 결과, Spectabilis가 Conspicua보다 Succinea 변이형에 높은 유사성을 보였다. 색상에 연관된 AFLP 후보 지표를 기준으로 sequence characterized amplified region (SCAR) 지표로 변환하여 9 개의 AFLP 분자지표들 가운데에서 5 개만이 SCAR 지표로 전환될 수 있었으며, 이를 통해 AFLP 지표가 무당벌레의 색상과 연관되어 있는지 확인할 수 있었다.