• 한국발생생물학회:학술대회논문집
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• 한국발생생물학회 2003년도 제3회 국제심포지움 및 학술대회
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• pp.94-94
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• 2003

Rotavirus는 유아나 어린아이들에게 가장 일반적으로 나타나는 심한 위장염의 원인자이며 설사로 인한 심한 탈수 증세를 일으켜 급속히 성장하는 유아의 균형적인 영양 공급을 방해함으로써 유아들의 발육과 성장 그리고 심하면 생명에 커다란 영향을 미치게 된다. 한편 모유로 키운 유아들은 설사병의 낮은 발병율과 연관이 있었다. 특히 모유의 뮤신 복합체는 rotavirus에 특이적으로 결합하여 항 바이러스활동을 보여주는 것으로 나타났다. 이러한 배경에서 본 연구는 human breast tissue로부터 lactadherin의 cloning 및 sequence 분석을 통하여 유전자의 다양성을 조사하기로 하였다. 한국 여성 9명의 유두 근처 조직에서 lactadherin을 cloning하여 그 sequence를 보고 된 서양여성의 염기서열과 비교 분석결과 여러 곳에서 single nucleotide variation이 발견되었고 본 연구에서 클론한 lactadherin(31bp-1518bp)의 염기서열과 보고된 서양여성 lactadherin gene의 SNP와 비교하였을 때 8개의 SNP중 3부분만이 일치한다는 것을 확인하였다. 또한 같은 조직중 정상 조직과 암 조직 부분에서 각각 lactadherin을 클론하여 염기서열을 비교 분석하였는데 정상 조직에서 2곳의 silent mutation있었고 암조직에서 2곳의 mutation과 1곳의 silent mutation을 발견하였으며 전체 적으로 정상조직과 암 조직 부분에서 lactadherin을 clone하여 염기서열을 분석해본 결과 암조직일수록 유전자의 변이 비율이 높다는 것을 알 수 있었다. 그리고 동일한 염기서열 상에서 많은 변이가 일어났는데 286dp(A->C), 1418dp(G->C)은 mutation이었고 327dp (A->G), 454(C->T)은 silent mutation이었다. 그 외 DNA상에서 여러 부근에 변이가 존재하였는데 이 결과로 보아 coding region에 위치한 cSNP 중 amino acid 변화를 일으켜 protein structure 또는 function에 영향을 줄 수 있는 non-synonymous cSNP 일 것으로 예상되어지며 natural selection의 영향을 받고 있음을 암시하고 있다. 본 연구에서 관찰되어진 각각의 염기 서열의 변이는 한국 사람이 가지는 lactadherin gene의 cSNP의 일부라고 판단하였다.

• 한국가금학회지
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• 제45권3호
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• pp.209-217
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• 2018

The innate immune recognition is based on the detection of microbial products. Toll-like receptors (TLRs) located on the cell surface and the endosome senses microbial components and nucleic acids, respectively. Chicken TLRs mediate immune responses by sensing ligands from pathogens, have been studied as immune adjuvants to increase the efficacy of vaccines. Single nucleotide polymorphisms (SNPs) of TLR3 and TLR4 genes in chicken were associated with resistance and susceptibility to viral infection. In this study, SNPs of chTLR3 and chTLR4 genes were retrieved from public database and annotated with chicken reference genome. Three-dimensional models of the chTLR3 and chTLR4 proteins were built using a Swiss modeler. We identified 35 and 13 nsSNPs in chTLR3 and chTLR4 genes respectively. Sorting Intolerant from Tolerant (SIFT) and Polymorphism Phenotyping v2 (Polyphen-2) analyses, suggested that, out of 35 and 13 nsSNPs, 4 and 2 SNPs were identified to be deleterious in chTLR3 and chTLR4 gene respectively. In chTLR3, 1 deleterious SNP was located in ectodomain and 3 were located in the Toll / IL-1 receptor (TIR) domain. Further structural model of chTLR3-TIR domain suggested that 1 deleterious SNP be present in the B-B loop region, which is important for TIR-TIR domain interactions in the downstream signaling. In chTLR4, the deleterious SNPs were located both in the ectodomain and TIR domain. SNPs predicted for chTLR3 and chTLR4 in this study, might be related to resistance or susceptible to viral infection in chickens. Results from this study will be useful to develop the effective measures in chicken against infectious diseases.

• Journal of the Korean Data and Information Science Society
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• 제20권4호
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• pp.639-647
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• 2009

컴퓨터공학의 발전으로 인해, 여러 개의 변수가 존재하는 비선형 문제와 같은 최적해 탐색과 최적화에 사용되는 유전자 알고리즘은 많은 분야에서 활발하게 응용되고 있다. 그 중, 데이터마이닝분야에서 유전자 알고리즘을 이용하여 정확도를 최대로 하는 입력변수 선택방법과 여러 예측모형을 통합하는 방법 등이 제시되었다. 한편, 우리나라 축산업을 대표하는 한우의 유전자원 보존과 능력향상을 위해서는 다음세대에 유전이 되는 단일염기다형성에서 특정 유전자형을 가진 한우가 경제형질이 우수한지를 찾아낼 필요가 있다. 이에 따라, 유전자 알고리즘을 이용하여 한우의 경제형질에 가장 많은 영향을 주는 단일염기다형성 조합마커의 유전자형을 선택하는 방법을 제시하였다. 그리고 실제 한우 유전 데이터에 적용하여 주요 단일염기다형성 조합마커에서 우수 유전자형들을 선별하였다.

• Asian-Australasian Journal of Animal Sciences
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• 제28권2호
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• pp.166-170
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• 2015

Foot-and-mouth disease (FMD) is a highly contagious disease affecting cloven-hoofed animals and causes severe economic loss and devastating effect on international trade of animal or animal products. Since FMD outbreaks have recently occurred in some Asian countries, it is important to understand the relationship between diverse immunogenomic structures of host animals and the immunity to foot-and-mouth disease virus (FMDV). We performed genome wide association study based on high-density bovine single nucleotide polymorphism (SNP) chip for identifying FMD resistant loci in Holstein cattle. Among 624532 SNP after quality control, we found that 11 SNPs on 3 chromosomes (chr17, 22, and 15) were significantly associated with the trait at the p.adjust <0.05 after PERMORY test. Most significantly associated SNPs were located on chromosome 17, around the genes Myosin XVIIIB and Seizure related 6 homolog (mouse)-like, which were associated with lung cancer. Based on the known function of the genes nearby the significant SNPs, the FMD resistant animals might have ability to improve their innate immune response to FMDV infection.

• Plant Biotechnology Reports
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• 제4권3호
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• pp.223-228
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• 2010

Schizonepeta tenuifolia (Korean name "Hyung- Gae") is an oriental medicinal plant that is widely used in Korea, China and Japan. S. tenuifolia (Hyung-Gae) has many pharmacological activities and is mostly used for many medicinal preparations. The dried aerial part (spikes and stems) of three oriental medicinal plants, S. tenuifolia (Hyung-Gae), Agastache rugosa (Kwhak-Hyang) and Elsholtzia ciliata (Hyang-Yoo) belonging to the same family, mint family Labiaceae, have such similar shape and smell that it is difficult to differentiate between them. The trnL-F regions of chloroplast DNA of the three medicinal plants were sequenced and used as targets in multiplex PCR reaction to identify S. tenuifolia. After alignment of trnL-F sequences of the authenticated plant samples, one single nucleotide polymorphism (SNP) specific to S. tenuifolia was found. Based on this SNP, a new primer was designed that specifically amplifies the trnL-F region of S. tenuifolia. The established multiplex-PCR was proven to be effective in the differentiation of commercial S. tenuifolia samples from A. rugosa and E. ciliata. This rapid and accurate molecular method is highly promising for use in the food industry.

• Asian-Australasian Journal of Animal Sciences
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• 제31권2호
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• pp.180-188
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• 2018

Objective: The aim of this study was to investigate the effect of single nucleotide polymorphisms (SNPs) of the melanogenesis associated transcription factor (MITF) and dopachrome tautomerase (DCT) genes on plumage coloration in Asian native duck breeds. MITF encodes a protein for microphthalmia-associated transcription factor, which regulates the development and function of melanocytes for pigmentation of skin, hair, and eyes. Among the tyrosinase-related family genes, DCT is a pigment cell-specific gene that plays important roles in the melanin synthesis pathway and the expression of skin, feather, and retina color. Methods: Five Asian duck varieties (black Korean native, white Korean native, commercial Peking, Nageswari, and Bangladeshi Deshi white ducks) were investigated to examine the polymorphisms associated with plumage colors. Among previously identified SNPs, three synonymous SNPs and one indel of MITF and nine SNPs in exon regions of DCT were genotyped. The allele frequencies for SNPs of the black and white plumage color populations were estimated and Fisher's exact test was conducted to assess the association between the allele frequencies of these two populations. Results: Two synonymous SNPs (c.114T>G and c.147T>C) and a 14-bp indel (GCTGCAAAC AGATG) in intron 7 of MITF were significantly associated with the black- and white-colored breeds (p<0.001). One non-synonymous SNP [c.938A>G (p.His313Arg)] in DCT, was highly significantly associated (p<0.001) and a synonymous SNP (c.753A>G) was significantly associated (p<0.05) with black and white color plumage in the studied duck populations. Conclusion: The results of this study provide a basis for further investigations of the associations between polymorphisms and plumage color phenotypes in Asian duck breeds.

• Asian-Australasian Journal of Animal Sciences
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• 제28권3호
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• pp.328-333
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• 2015

A genome wide association study was conducted using estimated breeding value (EBV) for milk production traits from 1st to 4th lactation. Significant single nucleotide polymorphism (SNP) markers were selected for each trait and the differences were compared by lactation. DNA samples were taken from 456 animals with EBV which are Holstein proven bulls whose semen is being sold or the daughters of old proven bulls whose semen is no longer being sold in Korea. High density genome wide SNP genotype was investigated and the significance of markers associated with traits was tested using the breeding value estimated by a multiple lactation model as a dependent variant. As the result of significance comparisons by lactations, several differences were found between the first lactation and subsequent lactations (from second to 4th lactation). A similar trend was noted in mean deviation and correlation of the estimated effects by lactation. Since there was a difference in the genes associated with EBV for each trait between first and subsequent lactations, a multi-lactation model in which lactation is considered as a different trait is genetically useful. Also, significant markers in all lactations and common markers for different traits were detected, which can be used as markers for quantitative trait loci exploration and marker assisted selection in milk production traits.

• 한국작물학회:학술대회논문집
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• 한국작물학회 2017년도 9th Asian Crop Science Association conference
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• pp.146-146
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• 2017

The pod shattering or dehiscence is essential for the propagation of pod-bearing plant species in the wild, but it causes significant yield losses during harvest of domesticated crop plants. Identifying novel molecular makers, which are linked to seed-shattering genes, is needed to employ the molecular marker-assisted selection for efficiently developing shattering-resistant soybean varieties. In this study, a genetic linkage map was constructed using 115 recombinant inbred lines (RILs) developed from crosses between the pod shattering susceptible variety, Keunol, and resistant variety, Sinpaldal. A 180 K Axiom(R) SoyaSNPs data and pod shattering data from two environments in 2001 and 2015 were used to identify quantitative trait loci (QTL) for pod shattering. A major QTL was identified between two flanking single nucleotide polymorphism (SNP) markers, AX-90320801 and AX-90306327 on chromosome 16 with 1.3 cM interval, 857 kb of physical range. In sequence, genotype distribution analysis was conducted using extreme phenotype RILs. This could narrow down the QTL down to 153 kb on the physical map and was designated as qPDH1-KS with 6 annotated gene models. All exons within qPDH1-KS were sequenced and the 6 polymorphic SNPs affecting the amino acid sequence were identified. To develop universally available molecular markers, 38 Korean soybean cultivars were investigated by the association study using the 6 identified SNPs. Only two SNPswere strongly associated with the pod shattering. These two identified SNPs will help to identify the pod shattering responsible gene and to develop pod shattering-resistant soybean plants using marker-assisted selection.

• Journal of Animal Science and Technology
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• 제53권6호
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• pp.511-516
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• 2011

Fas gene known to associate with intramuscular fat content in Korean cattle was selected for DNA marker development. Fas (APO-1, CD95), a member of the tumor necrosis factor (TNF) receptor superfamily, is a cell membrane protein that mediates apoptosis (programmed cell death). We discovered single nucleotide polymorphisms (SNPs) within Fas gene in order to develop novel DNA markers at genomic level. Of this gene to search for SNP, sequences of whole exon and 1kb range of both front and back of the gene using 24 cattle were determined by direct-sequencing methods. As a result, 16 SNPs in exon, 37 SNPs in intron and 2 SNPs in promoter region, a total of 55 SNPs were discovered. In these SNPs, thirty-one common polymorphic sites were selected considering their allele frequencies, haplotype-tagging status and Linkage Disequilibrium (LD) for genotyping in larger-scale subjects. Selected SNPs were confirmed genotype through SNaPshot method (n=274) and were examined for possible genetic association of Fas polymorphisms with carcass weight (CWT), eye muscle area (EMA), and backfat thickness (BF). So, the SNP have been identified significant g.-12T>G, g.1112T>G and g.32548T>C. These results suggest that polymorphism of Fas gene was associated with meat quality traits in Hanwoo.

• Asian-Australasian Journal of Animal Sciences
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• 제32권3호
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• pp.341-349
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• 2019

Objective: Internal organs indirectly affect economic performance and well-being of animals. Study of internal organs during later layer period will allow full utilization of layer hens. Hence, we conducted a genome-wide association study (GWAS) to identify potential quantitative trait loci or genes that potentially contribute to internal organ weight. Methods: A total of 1,512 chickens originating from White Leghorn and Dongxiang Blue-Shelled chickens were genotyped using high-density Affymetrix 600 K single nucleotide polymorphism (SNP) array. We conducted a GWAS, linkage disequilibrium analysis, and heritability estimated based on SNP information by using GEMMA, Haploview and GCTA software. Results: Our results displayed that internal organ weights show moderate to high (0.283 to 0.640) heritability. Variance partitioned across chromosomes and chromosome lengths had a linear relationship for liver weight and gizzard weight ($R^2=0.493$, 0.753). A total of 23 highly significant SNPs that associated with all internal organ weights were mainly located on Gallus gallus autosome (GGA) 1 and GGA4. Six SNPs on GGA2 affected heart weight. After the final analysis, five top SNPs were in or near genes 5-Hydroxytryptamine receptor 2A, general transcription factor IIF polypeptide 2, WD repeat and FYVE domain containing 2, non-SMC condensin I complex subunit G, and sonic hedgehog, which were considered as candidate genes having a pervasive role in internal organ weights. Conclusion: Our findings provide an understanding of the underlying genetic architecture of internal organs and are beneficial in the selection of chickens.