• Animal Bioscience
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• 제37권5호
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• pp.826-831
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• 2024

Objective: The major histocompatibility complex in chicken demonstrates a great range of variations within varities, breeds, populations and that can eventually influence their immuneresponses. The preset study was conducted to understand the major histocompatibility complex-B (MHC-B) variability in five major populations of Bangladesh native chicken: Aseel, Hilly, Junglefowl, Non-descript Deshi, and Naked Neck. Methods: These five major populations of Bangladesh native chicken were analyzed with a subset of 89 single nucleotide polymorphisms (SNPs) in the high-density MHC-B SNP panel and Kompetitive Allele-Specific polymerase chain reaction genotyping was applied. To explore haplotype diversity within these populations, the results were analyzed both manually and computationally using PHASE 2.1 program. The phylogenetic investigations were also performed using MrBayes program. Results: A total of 136 unique haplotypes were identified within these five Bangladesh chicken populations, and only one was shared (between Hilly and Naked Neck). Phylogenetic analysis showed no distinct haplotype clustering among the five populations, although they were shared in distinct clades; notably, the first clade lacked Naked Neck haplotypes. Conclusion: The present study discovered a set of unique MHC-B haplotypes in Bangladesh chickens that could possibly cause varied immune reponses. However, further investigations are required to evaluate their relationships with global chicken populations.

• Clinical and Experimental Pediatrics
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• 제53권4호
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• pp.548-553
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• 2010

목 적: IgA 신병증은 소아들의 만성 사구체 신염 중에서 가장 흔하게 일어나며, HLA유전자는 다양한 염증성 질환과 자가면역질환과 연관이 있어 왔다. 이 연구에서는 한국인에서 건강한 대조군과 IgA 신병증 환자군을 비교하여 IgA 신병증 발생 감수성 및 병리, 임상 양상과 $HLA-G$ 유전자의 SNP와의 연관성에 관해 알아보고자 하였다. 방 법: 소아 IgA 신병증을 앓고 있는 174명의 환자군과 438명의 정상 대조군에서 $HLA-G$ 유전자의 promoter SNP (rs1736936과 rs2735022)를 분석하고 비교하였다. 또한 IgA 신병증 환자들을 단백뇨($4mg/m^2/hour$ 이하군과 이상군)의 유무, 족세포 돌기의 소실 유무, 간질의 섬유화 및 세뇨관 위축이나 미만성 사구체 경화와 같은 병리학적 소견상 진행성 질환의 표지자유무에 따라 하위그룹으로 나누어 비교하였다. 결 과: IgA 신병증 환자군과 정상 대조군 간의 HLA-G에서의 SNP (rs1736936과 rs2735022) 빈도에 대한 유의한 차이는 발견되지 않았다. 또한 단백뇨의 유무, 족세포 돌기의 소실 유무, 질환의 병리학적 진행 정도을 의미하는 표지자의 유무와 SNP사이에서도 유의한 연관성을 보이지는 않았다. 그러나, 일체 배형으로서 rs1736936과 rs2735022는 소아 IgA 신병증을 일으키는 감수성에 대해 통계학적으로 유의한 연관성을 나타내었다(haplotype T/C: dominant model OR 1.71, 95% CI 1.00-2.92, $P$=0.049; haplotype C/T: recessive model OR 0.54, 95% CI 0.31-0.94, $P$=0.030). 결 론: 이번 연구에서 $HLA-G$ 유전자의 SNP 중 rs1736936와 rs2735022로 이루어진 일체배형과 IgA 신병증의 발생간에 유의한 관계를 관찰하였으며, IgA 신병증 환자들의 단백뇨 발생 유무, 족세포 돌기의 소실 유무 및 질병 진행 정도로 구분된 하위그룹과 후보 SNP들간의 유의한 관계는 확인할 수 없었다.

• 한국정보과학회논문지:소프트웨어및응용
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• 제36권9호
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• pp.691-696
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• 2009

서론: 천식에는 아스피린 과민증 (aspirin hypersensitivity)에 따라 아스피린 불내성 (aspirin intolerant asthma, AIA)과 내성 천식 (aspirin tolerant asthma, ATA) 두 가지 유형이 있다. 천식과 관련된 유전적 위험 요인들은 집중적으로 또한 광범위하게 연구되고 있다. 그러나 단일염기다형성들의 조합의 효과에 대해서는 거의 평가되지 않았다. 본 논문에서는 두 유형의 천식 진단에 유용한 단일염기다형성의 최상의 조합을 찾는다. 방법: 본 논문에서는 246명의 천식환자들을 조사하였다. (94명은 아스피린 불내성 천식을 152명은 아스피린 내성 천식을 가지고 있다) 그리고 천식과 관련된 것으로 추측되는 25개의 단일염기다형성들을 분석하였다. 단일염기다형성의 조합의 정규상호정보 값을 계산하여 높은 정규상호정보 값을 갖는 단일염기다형성들의 조합을 선택하고 선택된 조합들의 예측 정확도를 지지벡터기계를 사용하여 계산하였다. 결과: 최상의 조합은 4개짜리이고 ALOX5_p1_1708, B2ADR_q1_46, CCR3_p1_520, CysLTR1_p1_534로 구성된 모델이다. 이것은 0.053의 정규상호정보 값과 71.14%의 ATA 질병에 대한 예측 정확도를 갖는다.

• Journal of Plant Biotechnology
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• 제45권1호
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• pp.9-16
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• 2018

DNA 바코딩 기술은 다양한 약용식물 종들의 기원을 확인하기 위해 폭넓게 이용되고 있는 연구방법이다. 그러나, 시중에 판매되고 있는 유사 식물종을 재료로 사용한 상품이나 혼재되어 있는 상품에서 확인하고자 하는 약용식물을 선별 가능한 실질적인 기술의 개발은 아직 많이 미흡한 실정이다. 최근에는 보다 신속하고 정확도가 높은 기술을 개발하고자 DNA barcoding (Bar) 기술과 high-resolution melting (HRM) curve pattern 분석기술을 혼합한 Bar-HRM 분석기술을 이용한 연구가 진행 중에 있다. 본 리뷰논문에서는 국제적인 시장에서 다양한 기원의 약용식물 판별에 실질적으로 적용 가능한 Bar-HRM 기술의 최근의 발전 과정과 그 이용에 대해서 정리하였다. 다양한 연구들을 통해서 일부 성공적인 결과들이 보고되고 있지만, 제한된 DNA 바코드 및 단일염기다형성(Single Nucleotide Polymorphism, SNP) 등 아직 해결되어야 할 과제들이 많다. 특히, 핵 내 바코드로는 ribosomal DNA의 internal transcribed sequence (ITS)단편 이외에는 보고된 사례가 한건도 없었다. 또한, 약용식물을 끓는 물로 추출하여 가공한 약탕, 잼, 젤리, 쥬스 등의 제품은 DNA 단편이 분해되어 분리가 안 되는 경우에는 DNA바코딩 기술을 적용하기가 곤란한 것으로 알려져 있으나 비교적 짧은 DNA단편이 요구되는 Bar-HRM 분석기술을 이용하여 일부 성공한 보고도 있어 향후 그 응용사례가 증가할 것으로 전망된다.

• Asian-Australasian Journal of Animal Sciences
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• 제21권11호
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• pp.1544-1550
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• 2008

The retinoids (vitamin A and its derivatives) play a critical role in vision, growth, reproduction, cell differentiation and embryonic development. Using the IMpRH panel, porcine cellular retinol binding protein genes 5 and 7 (RBP5 and RBP7) were assigned to porcine chromosomes 5 and 6, respectively. The complete coding sequences (CDS) of the RBP5 and RBP7 genes were amplified using the reverse transcriptase polymerase chain reaction (RT-PCR) method, and the deduced amino acid sequences of both genes were compared to human corresponding proteins. The mRNA distributions of the two genes in adult Wuzhishan pig tissues (lung, skeletal muscle, spleen, heart, stomach, large intestine, lymph node, small intestine, liver, brain, kidney and fat) were examined. A total of nine single nucleotide polymorphisms (SNPs) were identified in two genes. Three of these SNPs were analyzed using the polymerase chain reaction-restriction-fragment length polymorphism (PCR-RFLP) method in Laiwu, Wuzhishan, Guizhou, Bama, Tongcheng, Yorkshire and Landrace pig breeds. Association analysis of genotypes of these SNP loci with economic traits was done in our experimental populations. Significant associations of different genotypes of $RBP5-A/G^{63}$, $RBP5-A/G^{517}$ and $RPB5-T/C^{intron1-90}$ loci with traits including maximum carcass length (LM), minimum carcass length (LN), marbling score (MS), back fat thickness at shoulder (SBF), meat color score (MCS) and hematocrit (HCT) were detected. These SNPs may be useful as genetic markers in genetic improvement for porcine production.

• Journal of Animal Science and Technology
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• 제58권4호
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• pp.14.1-14.9
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• 2016

Background: Peroxisome proliferator-activated receptor gamma (PPARG), CCAAT/enhancer binding protein alpha (CEBPA) and retinoid X receptor alpha (RXRA) are nuclear transcription factors that play important roles in regulation of adipogenesis and fat deposition. The objectives of this study were to characterise the variability of these three candidate genes in a mixed sample panel composed of several cattle breeds with different meat quality, validate single nucleotide polymorphisms (SNPs) in a local crossbred population (Angus - Hereford - Limousin) and evaluate their effects on meat quality traits (backfat thickness, intramuscular fat content and fatty acid composition), supporting the association tests with bioinformatic predictive studies. Results: Globally, nine SNPs were detected in the PPARG and CEBPA genes within our mixed panel, including a novel SNP in the latter. Three of these nine, along with seven other SNPs selected from the Single Nucleotide Polymorphism database (SNPdb), including SNPs in the RXRA gene, were validated in the crossbred population (N = 260). After validation, five of these SNPs were evaluated for genotype effects on fatty acid content and composition. Significant effects were observed on backfat thickness and different fatty acid contents (P < 0.05). Some of these SNPs caused slight differences in mRNA structure stability and/or putative binding sites for proteins. Conclusions: PPARG and CEBPA showed low to moderate variability in our sample panel. Variations in these genes, along with RXRA, may explain part of the genetic variation in fat content and composition. Our results may contribute to knowledge about genetic variation in meat quality traits in cattle and should be evaluated in larger independent populations.

• Clinical and Experimental Pediatrics
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• 제55권10호
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• pp.388-392
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• 2012

Purpose: Single-nucleotide polymorphism (SNP) markers within LIN28B have been reported to be related to the timing of pubertal growth. However, no study has investigated the frequency of genetic markers in girls with precocious puberty (PP) or early puberty (EP). This study aimed to determine the frequency of putative genetic markers in girls with PP or EP. Methods: Genomic DNAs were obtained from 77 and 109 girls that fulfilled the criteria for PP and EP, respectively. The controls in this study were 144 healthy volunteers between 20 and 30 years of age. The haplotypes were reconstructed using 11 SNPs of LIN28B, and haplotype association analysis was performed. The haplotype frequencies were compared. Differences in the clinical and laboratory parameters were analyzed according to the haplotype dosage. Results: Eleven SNPs in LIN28B were all located in a block that was in linkage disequilibrium. The haplotype could be reconstructed using 2 representative SNPs, rs4946651 and rs369065. The AC haplotype was less frequently observed in the PP group than in the controls (0.069 vs. 0.144, P=0.010). The trend that girls with non-AC haplotypes tended to have earlier puberty onset (P=0.037) was illustrated even in the EP+PP patient group by Kaplan-Meier analysis. Conclusion: The results of the present study showed that non-AC haplotypes of LIN28B had a significant association with PP in girls.

• Genomics & Informatics
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• 제8권3호
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• pp.108-115
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• 2010

Hypertension is the most prevalent disease worldwide and is itself a risk factor for cerebral, cardiac, and renal diseases. The inconsistency of candidate genes suggested by previous genomewide association studies (GWASs) may be due to not only differences in study design and genetic or environmental background but also the difference in the power of analysis between continuous traits and discrete traits. We analyzed 352,228 single nucleotide polymorphisms (SNPs) in 8842 unrelated Koreans obtained from Ansan and Ansung cohorts. We performed a series of GWA analyses using three different phenotype models; young hypertensive cases (278 subjects) versus elderly normotensive controls (680 subjects); the upper 25% (2211 hypertensive cases) versus the lower 25% of the SBP distribution (2211 hypotensive controls); and finally SBP and DBP as continuous traits (8842 subjects). The numbers of young hypertensive cases and elderly normotensive controls were not large enough to achieve genomewide significance. The model comparing the upper 25% subjects to the lower 25% of subjects showed a power that was approximate to that of QTL analysis. Two neighboring SNPs of the ATP2B1 gene, rs17249754 (SBP, p=$2.53^{-10}$; DBP, p=$1.28{\times}10^{-8}$) and rs7136259 (SBP, p=$1.30{\times}10^{-9}$; DBP, p=$6.41{\times}10^{-8}$), were associated with both SBP and DBP. Interestingly, a SNP of the RPL6 gene, rs11066280, revealed a significant genomewide association with SBP in men only (p=$3.85{\times}10^{-8}$), and four SNPs located near the MAN2A1 gene showed a strong association with DBP only in elderly men aged 60-70 years (e.g., rs6421827, p=$4.86{\times}10^{-8}$). However, we did not observe any gene variant attaining genomewide significance consistently in the three phenotype models except for the ATP2B1 gene variants. In general, the association signal with blood pressure was stronger in women than in men. Genes identified in GWASs are expected to open the way for prevention, early diagnosis, and personalized treatment of hypertension.

• Journal of Animal Science and Technology
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• 제53권5호
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• pp.389-395
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• 2011

본 연구는 지방산의 합성의 완성 및 지방세포의 성장 및 합성에 영향을 미치는 FASN과 ACACA 유전자내의 단일염기변이(SNP)들을 한우의 도체형질에 미치는 영향을 조사하기 위해 수행되었다. 한우 능력평가집단 425두와 농협 축산연구원에서 제공받은 632두를 대상으로 FASN 유전자내의 4개(g.11280A>G, g.16024A>G, g.16039T>C, g.17924A>G)의 단일염기변이들과 ACACA 유전자내의 1개(g.2274G>A) 단일염기변이들이 도체형질에 미치는 효과를 분석하였다. 한우능력평가집단에서 FASN g.17924A>G는 도체중과 등지방두께에 유의적인 연관성을 나타내었으며, ACACA g.2274G>A는 배장근 단면적에 유의적인 연관성을 나타내었다. 농협 축산연구원의 샘플에서도 FASN g.17924A>G는 도체중에서 ACACA g.2274G>A는 배장근 단면적에서 동일한 유의적인 연관성이 관찰되었다. 한우 능력평가집단과 농협 축산연구원 샘플을 통합하여 FASN 유전자 g.17924A>G 와 ACACA 유전자 g.2274G>A 변이를 분석한 결과에서는 FASN g.17924A>G는 도체중과 등지방두께에 유의적인 연관성이 나타났으며, ACACA g.2274G>A는 등지방두께에서 유의적인 연관성을 나타내었다. 또한 FASN g.17924A>G와 ACACA g.2274G>A 의 유전자형조합에 따른 분석에서 도체중과 근내지방도에서 상호작용효과가 추정되었으며, 도체중과 근내지방도에 유의적인 상가적 효과를 나타내었다. FASN g.17924G>A의 GG 유전자형과 ACACA g.2274A>G의 GG 유전자형의 조합을 가진 개체는 다른 유전자형 조합을 가진 개체보다 높은 도체중과 근내지방도를 발현하는 개체인 것으로 관찰되었다(P<0.05). 본 연구의 결과는 두 유전자내의 단일염기변이들을 육량과 육질이 우수한 송아지 생산에 활용될 수 있을 것으로 사료된다.

• Genomics & Informatics
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• 제16권2호
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• pp.36-41
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• 2018

Kawasaki disease (KD) is an acute febrile vasculitis predominately affecting infants and children. The dominant incidence age of KD is from 6 months to 5 years of age, and the incidence is unusual in those younger than 6 months and older than 5 years of age. We tried to identify genetic variants specifically associated with KD in patients younger than 6 months or older than 5 years of age. We performed an age-stratified genome-wide association study using the Illumina HumanOmni1-Quad BeadChip data (296 cases vs. 1,000 controls) and a replication study (1,360 cases vs. 3,553 controls) in the Korean population. Among 26 candidate single nucleotide polymorphisms (SNPs) tested in replication study, only a rare nonsynonymous SNP (rs4365796: c.1106C>T, p.Thr369Met) in the lymphoid enhancer binding factor 1 (LEF1) gene was very significantly associated with KD in patients younger than 6 months of age (odds ratio [OR], 3.07; $p_{combined}=1.10{\times}10^{-5}$), whereas no association of the same SNP was observed in any other age group of KD patients. The same SNP (rs4365796) in the LEF1 gene showed the same direction of risk effect in Japanese KD patients younger than 6 months of age, although the effect was not statistically significant (OR, 1.42; p = 0.397). This result indicates that the LEF1 gene may play an important role as a susceptibility gene specifically affecting KD patients younger than 6 months of age.