• 제목/요약/키워드: BTA6

검색결과 37건 처리시간 0.026초

Multifactor Dimensionality Reduction (MDR) Analysis to Detect Single Nucleotide Polymorphisms Associated with a Carcass Trait in a Hanwoo Population

  • Lee, Jea-Young;Kwon, Jae-Chul;Kim, Jong-Joo
    • Asian-Australasian Journal of Animal Sciences
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    • 제21권6호
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    • pp.784-788
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    • 2008
  • Studies to detect genes responsible for economic traits in farm animals have been performed using parametric linear models. A non-parametric, model-free approach using the 'expanded multifactor-dimensionality reduction (MDR) method' considering high dimensionalities of interaction effects between multiple single nucleotide polymorphisms (SNPs), was applied to identify interaction effects of SNPs responsible for carcass traits in a Hanwoo beef cattle population. Data were obtained from the Hanwoo Improvement Center, National Agricultural Cooperation Federation, Korea, and comprised 299 steers from 16 paternal half-sib proven sires that were delivered in Namwon or Daegwanryong livestock testing stations between spring of 2002 and fall of 2003. For each steer at approximately 722 days of age, the Longssimus dorsi muscle area (LMA) was measured after slaughter. Three functional SNPs (19_1, 18_4, 28_2) near the microsatellite marker ILSTS035 on BTA6, around which the QTL for meat quality were previously detected, were assessed. Application of the expanded MDR method revealed the best model with an interaction effect between the SNPs 19_1 and 28_2, while only one main effect of SNP19_1 was statistically significant for LMA (p<0.01) under a general linear mixed model. Our results suggest that the expanded MDR method better identifies interaction effects between multiple genes that are related to polygenic traits, and that the method is an alternative to the current model choices to find associations of multiple functional SNPs and/or their interaction effects with economic traits in livestock populations.

A Restricted Partition Method to Detect Single Nucleotide Polymorphisms for a Carcass Trait in Hanwoo

  • Lee, Ji-Hong;Kim, Dong-Chul;Kim, Jong-Joo;Lee, Jea-Young
    • Asian-Australasian Journal of Animal Sciences
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    • 제24권11호
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    • pp.1525-1528
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    • 2011
  • The purpose of this study was to detect SNPs that were responsible for a carcass trait in Hanwoo populations. A non-parametric model applying a restricted partition method (RPM) was used, which exploited a partitioning algorithm considering statistical criteria for multiple comparison testing. Phenotypic and genotypic data were obtained from the Hanwoo Improvement Center, National Agricultural Cooperation Federation, Korea, in which the pedigree structure comprised 229 steers from 16 paternal half-sib proven sires that were born in Namwon or Daegwanryong livestock testing station between spring of 2002 and fall of 2003. A carcass trait, longissimus dorsi muscle area for each steer was measured after slaughter at approximately 722 days. Three SNPs (19_1, 18_4 and 28_2) near the microsatellite marker ILSTS035 on BTA6, around which the quantitative trait loci (QTL) for meat quality were previously detected, were used in this study. The RPM analyses resulted in two significant interaction effects between SNPs (19_1 and 18_4) and (19_1 and 28_2) at ${\alpha}$ = 0.05 level. However, under a general linear (parametric) model no interaction effect between any pair of the three SNPs was detected, while only one main effect for SNP19_1 was found for the trait. Also, under another non-parametric model using a multifactor dimensionality reduction (MDR) method, only one interaction effect of the two SNPs (19_1 and 28_2) explained the trait significantly better than the parametric model with the main effect of SNP19_1. Our results suggest that RPM is a good alternative to model choices that can find associations of the interaction effects of multiple SNPs for quantitative traits in livestock species.

Characterization and Mapping of the Bovine FBP1 Gene

  • Guo, H.;Liu, W-S.;Takasuga, A.;Eyer, K.;Landrito, E.;Xu, Shang-zhong;Gao, X.;Ren, H-Y.
    • Asian-Australasian Journal of Animal Sciences
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    • 제20권9호
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    • pp.1319-1326
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    • 2007
  • Fructose-1,6-bisphosphatase (FBP1) is a key regulatory enzyme of gluconeogenesis that catalyzes the hydrolysis of fructose-1,6-bisphosphate to generate fructose-6-phosphate and inorganic phosphate. Deficiency of fructose-1, 6-bisphosphatase is associated with fasting hypoglycemia and metabolic acidosis. The enzyme has been shown to occur in bacteria, fungi, plants and animals. The bovine FBP1 gene was cloned and characterized in this study. The full length (1,241 bp) FBP1 mRNA contained an open reading frame (ORF) encoding a protein of 338 amino acids, a 63 bp 5' untranslated region (UTR) and a 131 bp 3' UTR. The bovine FBP1 gene was 89%, 85%, 82%, 82% and 74% identical to the orthologs of pig, human, mouse, rat and zebra fish at mRNA level, and 97%, 96%, 94%, 93% and 91% identical at the protein level, respectively. This gene was broadly expressed in cattle with the highest level in testis, and the lowest level in heart. An intronic single nucleotide polymorphism (SNP) (A/G) was identified in the $5^{th}$ intron of the bovine FBP1 gene. Genotyping of 133 animals from four beef breeds revealed that the average frequency for allele A (A-base) was 0.7897 (0.7069-0.9107), while 0.2103 (0.0893-0.2931) for allele B (G-base). Our preliminary association study indicated that this SNP is significantly associated with traits of Average Daily Feed Intake (ADFI) and Carcass Length (CL) (p<0.01). In addition, the FBP1 gene was assigned on BTA8 by a hybrid radiation (RH) mapping method.

식이지방의 종류와 L-arginine 보충이 당뇨쥐의 ENdothelium 기능 및 체내 지질대사에 미치는 영향 (Effect of Dietary Fat Sources and L-arginine Supplementation on Endothelial function and Lipid Metabolism in Streptozotocin-Induced Diabetic Rats)

  • 장문정;김연중;김명환
    • Journal of Nutrition and Health
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    • 제35권1호
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    • pp.5-14
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    • 2002
  • Alteration in the syntesis or enhanced inactivation of nitric oxide(NO) can induce impairment of endothelial cell function. Insulin dependent diabetes mellitus(IDDM) is characterized by impaired endothelial function and vascular disease. NO is produced through L-arginine pathway To elucidate the hypothesis that the decreased production on NO in IDDM reflects vascular damage and the NO production can be manipulated by either dietary fat(7% of kg diet) or the oral supplementation with L-arginine(2g/kg bw), plasma markers for vascular endothelial damage and plasma lipid profiles were measured in streptozotocin(STZ)-induced diabetic rats. Diabetic or normal Sprague-Dawley rats were fed 6 different experimental diets for 4 weeks(SO : soybean oil, SOA: soybean oil + L-arginine supplementation, BT : beef tallow, BTA_ beef tallow + L-arginine supplementation, OV olive oil, OVA : olive oil + L-arginine supplementation). Plasma glucose, total cholesterel, HDL-cholesterol, LDL-cholesterol and triglyceride were measured. Endothelial markers, plasma von Willebrand factor(vWf), thromboxane B$_2$, and 6-keto PGF1$\alpha$ of aorta were measured by ELISA. Plasma NO production was evaluated through the measurement of nitrite by EIA. Feeding saturated fatty acid(SFA, BT) increased relative liver size(RLS) in diabetic rats compared to either polyunsatunted fatty acid(PUFA, SO) or monounsaturated fatty acid(MUFA, OV) The supplementation of L-arginine inhibited the liver and kidney enlargement in olive oil find diabetic rats. Plasma glucose was lower in diabetic animal find the olive oil compared to fed beef tallow and the supplementation L-arginine decreased it in diabetic rats find beef tallow significantly(p < 0.05). Plasma TXB$_2$ levels were increased due to diabetes and the value of beef tallow group showed highest value. Plasma vWf concentration of beef tallow group was higher value in normal rats and was elevated more in diabetes. In diabetic groups, the vWf concentration of olive oil group was lower than beef tallow or soybean oil group. The supplementation of L-arginine in diabetic rats decreased plasma TXB$_2$ and vWf levels significantly(p < 0.05). NO production was higher in normal olive oil fed rats and was tend to be decreased in diabetic rats and the supplementation of L-arginine recovered to normal value(p < 0.05), Olive oil supplemented with L-arginine tended to lower plasma total cholesterol and LDL-cholesterol after 4 week treatment. These results suggest that generalized vascular endothelial changes based on plasma TXB$_2$and vWf occurs in diabetic rats. and olive oil with L-arginine supplementation contributes to a better control of the hyperglycemia, endothelial changes and hypercholesterolemia accompanying diabetes as compared with beef tallow or soy bean oil in this rat model.

전장 유전체 연관분석을 통한 한우 성장 연관 양적형질좌위 (QTL) 탐색 (Genome Wide Association Study to Identity QTL for Growth Taits in Hanwoo)

  • 이승환;임다정;장길원;조용민;최봉환;김시동;오성종;이준헌;윤두학;박응우;이학교;홍성구;양보석
    • Journal of Animal Science and Technology
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    • 제54권5호
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    • pp.323-329
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    • 2012
  • 본 연구는 한우 거세우 266두에서 유전자형 결정이 완료된 4,522개의 SNP를 이용하여 한우 성장형질 (6, 12, 18 및 24개월령 체중)에 대한 양적형질좌위 (QTL)을 탐색 하였다. 각 SNP와 성장형질과의 연관성 분석은 회귀분석 (single marker regression)을 이용하여 수행하였으며, 통계적 유의성은 P-value (P<0.001)로 설정하였다. 그 결과, 6개월체중에서 3개 좌위, 12개월 체중에서는 5개 좌위, 18개월체중에서 5개좌위 그리고 24개월체중에서 4개 좌위가 통계적 유의차를 보였다. 통계적 유의차를 보인 SNP의 상가적 유전분산을 분석한 결과, 몇몇 SNP에서는 6~11% 정도의 상가적 유전효과를 보였으며, 대부분의 SNP들은 2~5%로 매우 작은 효과를 보였다.

Loop와 HPLC Purification 방법보다 더 높은 비방사능을 보여주는 카트리지 Methylation과 Purification을 이용한 손쉬운 [ 11C]PIB 합성 (Facile [11C]PIB Synthesis Using an On-cartridge Methylation and Purification Showed Higher Specific Activity than Conventional Method Using Loop and High Performance Liquid Chromatography Purification)

  • 이용석;조용현;이홍재;이윤상;정재민
    • 핵의학기술
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    • 제22권2호
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    • pp.67-73
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    • 2018
  • $[^{11}C]PIB$는 베타아밀로이드($A{\beta}\;plague$)라는 변성 단백질에 결합하여 뇌의 기능과 기억력을 서서히 감퇴시키는 비가역적인 질환인 치매를 조기에 감별할 수 있는 대표적인 방사성의약품이다. 지금까지 많은 실험실에서 $[^{11}C]PIB$는 자동화합성장치에서 $[^{11}C]methyl\;iodide$$[^{11}C]methyl\;triflate$를 만든 다음 loop나 vial 방법을 사용하여 methylation을 한 다음 HPLC로 정제를 하는 것이다. 하지만 기존의 보고된 방법은 시간이 오래 걸리며, HPLC와 같은 복잡한 시스템을 필요로 하여 소규모 실험실에서 합성하기에 적합하지 않으며, 최종 product에서 에탄올 함량이 높다는 단점이 있었다. 이러한 단점을 보완하기 위하여 카트리지만을 사용하여 카트리지에서 methylation과 purification을 동시에 실시함으로써 합성 시간을 단축하고, 비방사능이 높고, 낮은 에탄올 함량을 가진 $[^{11}C]PIB$를 합성 가능한지 확인하고자 하였다. 가장 널리 사용하는 카트리지 6종(CM, HLB, Alumina, C18, tC18, tC18 environmental을 선택하여 screening test를 실시하였다. 6-OH-BTA-0 1 mg을 c-HXO에 녹인 다음 6개의 카트리지에 loading를 한 다음 0.5 M MSP(pH 5.1) 20 mL로 정제를 한 다음 최종 fraction을 받아서 analytical HPLC로 전구체 잔류량을 측정한 결과 hydrophobicity가 낮은 계열(CM, HLB, Alumina)의 카트리지에서는 완충액으로 정제를 하였을 때 잔류전구체의 양이 많았으나, 탄소함량이 많은 계열의 카트리지(C18, tC18, tC18 environmental)에서는 잔류전구체의 양이 CM, HLB, Alumina 카트리지에 비하여 상대적으로 적었다. 완충액의 정제 농도와 부피를 최적화 하기 위하여 screening test에서 가장 좋은 결과를 나타낸 C18 series cartridge를 가지고 추가 실험을 진행하였다. 인산완충액 농도를 10 mM, 20 mM, 30 mM, 40 mM, 50 mM, 250 mM, 500 mM로 변화시켰으며, 에탄올 함량은 20%와 30%로 하여 용출액을 분석하여서, $[^{11}C]PIB$를 카트리지로 합성하기 위한 최적의 조합은 tC18 environmental cartridge와 0.5 M MSP 20 mL인 것을 알 수 있었다. 기존에 보고된 방법과 cartridge를 비교한 결과, 합성시간에서는 각각 15 ~ 18min, 8 ~ 9 min이 소요되었으며, product activity는 각각 $4.1{\pm}1.4\;GBq$ (n=41), $3.8{\pm}0.9\;GBq$ (n=3), 방사화학적 수율(based on HPLC analysis of the crude product)에서는 $13.9{\pm}4.4%$ (n=41), $12.3{\pm}2.2%$ (n=3)로 별다른 차이가 없었으며, 비방사능에 있어서는 HPLC purification method가 $78.7{\pm}39.7\;GBq/{\mu}mol$ (n=41), cartridge method가 $420.6{\pm}20.4\;GBq/{\mu}mol$ (n=3)로 카트리지 방법이 기존 방법보다 더 좋은 결과를 나타내었다. 또한, 잔류 용매(c-HXO)도 vial or loop method와 별다른 차이가 없었으며, 에탄올 함량에 있어서는 70%(기존 방법)에서 30%(카트리지 방법)로 두 배 이상 함량이 적다는 사실을 알 수 있었다. 지금까지 알아본바와 같이 cartridge method는 reported method(HPLC purification)에 비하여 더 향상된 결과를 보여준다는 사실을 확인하였다.

한우에서 전장의 유전체 정보를 활용한 연관불평형 및 유효집단크기 추정에 관한 연구 (Estimation of Linkage Disequilibrium and Effective Population Size using Whole Genome Single Nucleotide Polymorphisms in Hanwoo)

  • 조충일;이준호;이득환
    • 생명과학회지
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    • 제22권3호
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    • pp.366-372
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    • 2012
  • 본 연구는 한우 유전체 전장에 존재하는 고밀도 단일염기다형을 DNA chip을 이용하여 각각의 유전자형을 구명하고, 동일염색체 내에 존재하는 각 표지인자쌍의 연관불평형을 성 염색체를 제외한 모든 상염색체에서 추정하여 물리적 거리별 연관불평형의 정도를 확인하고 이러한 결과를 이용하여 한우 집단의 유효집단 크기를 추정하기 위하여 실시하였다. 한우개량사업소에서 2005년부터 2008년까지 후대검정에 공시된 후보종모우 및 후대 검정우 288두에 대해 혈액을 채취하고 Bovine SNP 50 DNA Chip을 이용하여 유전자형을 분석하였으며, 총 51,582 표지인자 중 결측률이 10% 이상인 표지인자 1개 및 다형성이 없는 표지인자 10,730개에 대해 사전제거를 실시하고 남은 40,851개의 SNP표지인자를 본 분석에 활용하였다. 연구 결과, 성 염색체를 제외한 상 염색체의 총 SNP표지인자의 길이는 2,541.6 Mb였으며, 염색체별 평균 SNP표지인자간 거리는 0.55에서 0.74로 분포하였으며, EM알고리즘을 이용하여 염색체별 연관불평형을 추정해 보았을 때, 기존의 보고된 연구와 유사하게 표지인자간 거리가 짧을수록 높게 나타나는 지수형태의 그래프를 나타냈으며, SNP표지인자간 거리에 따른 $r^2$를 보면, 0 Mb에서 0.1 Mb일 때 0.136, 0.1-0.2 Mb에서 0.06로 나타났다. Luo (1998)의 연구결과를 한우에 적용시켰을 때, 전체분산의 5%이상 설명하는 양적형질좌위 발굴을 위해서 약 2,000두의 표현형 자료가 필요할 것으로 사료되었다. 또한 한우의 세대별 유효집단 크기에 대해 추정해 본 결과, 현재 한우의 유효집단크기는 84두로 추정되었고, 지금으로부터 약 50세대 이전의 유효집단 크기는 1,150두로 추정되었다. 가축에서 인공수정이 도입(1960년대)된 이 후 개량의 가속화로 인해 한우의 유효집단 크기가 급격히 감소한 것으로 사료되었다.