• Title, Summary, Keyword: SNP

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Association Analysis between Insulin-like Growth Factor Binding Protein 3 (IGFBP3) Polymorphisms and Carcass Traits in Cattle

  • Cheong, Hyun Sub;Yoon, Du-Hak;Kim, Lyoung Hyo;Park, Byung Lae;Lee, Hye Won;Namgoong, Sohg;Kim, Eun Mi;Chung, Eui Ryong;Cheong, Il-Cheong;Shin, Hyoung Doo
    • Asian-Australasian Journal of Animal Sciences
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    • v.21 no.3
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    • pp.309-313
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    • 2008
  • The insulin-like growth factor binding protein 3 (IGFBP3) has been investigated as a candidate gene for growth promoting effects in beef cattle and a modulator of IGF bioactivity. Previously, we have reported twenty two sequence variants discovered in Korean native cattle (Hanwoo). In this study, we examined the association between gene-specific polymorphisms of IGFBP3 and cold carcass weight (CW) and marbling score (MS) among Korean native cattle. Among twenty two polymorphisms, four common polymorphic sites (-854G>C, -100G>A, +421G>T and +3863C>A) were genotyped in our beef cattle (n = 437). Statistical analysis revealed that one common polymorphism in the promoter region (-854G>C) showed putative associations with MS (p = 0.03). IGFBP3 variation/haplotype information analyzed in this study will provide valuable information into strategies for the production of a commercial line of beef cattle.

Genome-Wide SNP Calling Using Next Generation Sequencing Data in Tomato

  • Kim, Ji-Eun;Oh, Sang-Keun;Lee, Jeong-Hee;Lee, Bo-Mi;Jo, Sung-Hwan
    • Molecules and Cells
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    • v.37 no.1
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    • pp.36-42
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    • 2014
  • The tomato (Solanum lycopersicum L.) is a model plant for genome research in Solanaceae, as well as for studying crop breeding. Genome-wide single nucleotide polymorphisms (SNPs) are a valuable resource in genetic research and breeding. However, to do discovery of genome-wide SNPs, most methods require expensive high-depth sequencing. Here, we describe a method for SNP calling using a modified version of SAMtools that improved its sensitivity. We analyzed 90 Gb of raw sequence data from next-generation sequencing of two resequencing and seven transcriptome data sets from several tomato accessions. Our study identified 4,812,432 non-redundant SNPs. Moreover, the workflow of SNP calling was improved by aligning the reference genome with its own raw data. Using this approach, 131,785 SNPs were discovered from transcriptome data of seven accessions. In addition, 4,680,647 SNPs were identified from the genome of S. pimpinellifolium, which are 60 times more than 71,637 of the PI212816 transcriptome. SNP distribution was compared between the whole genome and transcriptome of S. pimpinellifolium. Moreover, we surveyed the location of SNPs within genic and intergenic regions. Our results indicated that the sufficient genome-wide SNP markers and very sensitive SNP calling method allow for application of marker assisted breeding and genome-wide association studies.

Association between the Polymorphism of the Fatty acid binding protein 5 (FABP5) Gene within the BTA 14 QTL Region and Carcass/Meat Quality Traits in Hanwoo (한우 14번 염색체 QTL 영역내 Fatty acid binding protein 5 유전자의 다형성과 도체 및 육질 형질과의 관련성 분석)

  • Heo, Kang-Nyeong;Kim, Nam-Kuk;Lee, Seung-Hwan;Kim, Nam-Young;Jeon, Jin-Tae;Park, Eung-Woo;Oh, Sung-Jong;Kim, Tae-Hun;Seong, Hwan-Hoo;Yoon, Du-Hak
    • Journal of Animal Science and Technology
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    • v.53 no.4
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    • pp.311-317
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    • 2011
  • The aim of this study was to evaluate the association between economic traits of Korean cattle (Hanwoo) and genetic variation in fatty acid binding protein 5 (FABP5) gene within QTL region of carcass weight and marbling score traits on BTA 14. We sequenced for detection of single nucleotide polymorphism (SNP) with 24 unrelated Hanwoo samples and identified four SNPs (-1141A>G, 949A>G, 969A>G and 1085C>G). Relationship between the genotypes of 583 Hanwoo individuals by PCR-RFLP and economic traits were analyzed by the mixed regression model implemented in the ASReml program. As the result of statistical analysis, SNP1 (-1141A>G) showed significant effect (p<0.003) on marbling score (MS) and SNP2 (949A>G) showed significant effect (p<0.034) on eye muscle area (EMA). Further studies are required to validate the significant SNPs in a bigger population, but the SNPs (-1141A>G and 949A>G) of FABP5 could be a genetic marker to estimate molecular breeding value (MEBV) for carcass traits in Hanwoo.

Effects of nitric oxide on ascorbate-glutathione cycle enzymes activities in chinese cabbage leaves under paraquat-induced oxidative stress (Paraquat 유도 산화스트레스하의 배추 잎에서 Ascorbate-Glutathione 회로 효소의 활성도에 대한 산화질소 (Nitric oxide)의 효과)

  • Na, Ho-Gyun;Jin, Chang-Duck
    • Journal of Plant Biotechnology
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    • v.41 no.2
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    • pp.73-80
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    • 2014
  • Pretreatment of chinese cabbage leaves with $100{\mu}M$ sodium nitroprusside (SNP), a nitric oxide (NO) donor, effectively improved their tolerance to subsequent $2{\mu}M$ paraquat (PQ)-induced oxidative damage. The fresh weight, and chlorophyll and protein contents in primary leaves treated with PQ alone were noticeably reduced over 24 h light incubation. However, these leaf injury symptoms were significantly alleviated with $100{\mu}M$ SNP pretreatment for 3 h prior to PQ exposure. In additions, the increase of the contents of malondialdehyde (MDA) and $H_2O_2$ due to PQ exposure were significantly inhibited by SNP pretreatment. Together with the protective effects of SNP against PQ toxicity in leaves, the changes of ascorbate-glutathione cycle enzymes activities were examined. In the PQ alone treatment, the activities of APX, DHAR, and GR after 6 h incubation were rapidly reduced and showed 19%, 50% and 39% respectively, compared with those of the control. However, the decreases in these enzyme activities were significantly inhibited by SNP pretreatment. As a result, their activities were higher than those of PQ alone treatment by 5 times, 2 times, and 1.5 times, respectively, at 6 h incubation. Thereafter, these enzymes decrease their activities gradually showing high levels than those of PQ alone. Based on the above results, it can be assumed that the activation of ascorbate-glutathione cycle by SNP pretreatment in chinese cabbage leaves exposed to PQ can prevent $H_2O_2$ accumulation, thereby leading to protection against PQ-induced oxidative stress. Also, these results indicate that NO acts as an protectant against PQ stress in the leaves of chinese cabbage.

The Application of Single Nucleotide Polymorphism Markers for Discrimination of Sweet Persimmon Cultivars (단감 품종 판별을 위한 single nucleotide polymorphism 마커 적용 검정)

  • Park, Yeo Ok;Choi, Seong-Tae;Son, Ji-Young;Kim, Eun-Gyeong;Ahn, Gwang-Hwan;Park, Ji Hae;Joung, Wan-Kyu;Jang, Young Ho;Kim, Dong Wan
    • Journal of Life Science
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    • v.30 no.7
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    • pp.614-624
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    • 2020
  • The recent development of next-generation sequencing technology has enabled increased genomic analysis, but very few single nucleotide polymorphism (SNP) markers applicable to sweet persimmon (Diospyros kaki Thunb.) cultivars have been identified. In this study, SNP primers developed from five pollination-constant astringent (PCA) persimmons native to Korea were applied to discriminate between cultivars and verify their usability. The polymerase chain reactions of 19 SNP primers developed by Jung et al. were checked, with 11 primers finally selected. The other eight were very difficult to analyze in the agarose gel electrophoresis and QIAxcel Advanced System used in this experiment and were therefore excluded. The 11 SNP primers were applied through first and second verification to 76 cultivars and collection lines including 20 pollination-variant non-astringent (PVNA), 30 pollination-constant non-astringent (PCNA), 20 PCA, and six pollination-variant astringent (PVA). Of these, 38 were indistinguishable (eight PVNA, 18 PCNA, nine PCA, and three PVA). However, the results of applying the 11 SNP primers to new sweet persimmon cultivars, namely Gamnuri, Dannuri, Hongchoo, Jamisi, and Migamjosaeng, showed that they have the potential to be used as a unique marker for simultaneously determining between them.

A local search algorithm for predicting epistatic interactions of SNPs (복합 질환 관련 SNP 상호작용 예측을 위한 국소탐색 알고리즘)

  • Hong, Won-Pyo;Wee, Kyubum
    • Proceedings of the Korea Information Processing Society Conference
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    • pp.1395-1398
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    • 2010
  • 최근 GWAS(Genome-wide association study)로 인해 수십만 개의 SNP들이 사용 가능하게 되었다. 그러나 SNP 정보의 양이 방대하여 모든 SNP 조합을 검토하는 방식은 계산 비용이 클 뿐 아니라 오버피팅의 위험이 따른다. 본 논문에서는 필터링 기반 알고리즘인 SNPHarvester의 속도를 개선하고 평가함수를 상호정보량으로 대체하여 실험한다. 기존 SNPHarvester와 비교해 속도면에서 50%가 향상되었고 평가함수 면에서는 기존 SNPHarvester와 동일한 성능을 보였다.

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A Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Carcass Traits in Hanwoo Populations

  • Lee, Y.-M.;Han, C.-M.;Li, Yi;Lee, J.-J.;Kim, L.H.;Kim, J.-H.;Kim, D.-I.;Lee, S.-S.;Park, B.-L.;Shin, H.-D.;Kim, K.-S.;Kim, N.-S.;Kim, Jong-Joo
    • Asian-Australasian Journal of Animal Sciences
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    • v.23 no.4
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    • pp.417-424
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    • 2010
  • The purpose of this study was to detect significant SNPs for carcass quality traits using DNA chips of high SNP density in Hanwoo populations. Carcass data of two hundred and eighty nine steers sired by 30 Korean proven sires were collected from two regions; the Hanwoo Improvement Center of National Agricultural Cooperative Federation in Seosan, Chungnam province and the commercial farms in Gyeongbuk province. The steers in Seosan were born between spring and fall of 2006 and those in Gyeonbuk between falls of 2004 and 2005. The former steers were slaughtered at approximately 24 months, while the latter steers were fed six months longer before slaughter. Among the 55,074 SNPs in the Illumina bovine 50K chip, a total of 32,756 available SNPs were selected for whole genome association study. After adjusting for the effects of sire, region and slaughter age, phenotypes were regressed on each SNP using a simple linear regression model. For the significance threshold, 0.1% point-wise p value from F distribution was used for each SNP test. Among the significant SNPs for a trait, the best set of SNP markers were selected using a stepwise regression procedure, and inclusion and exclusion of each SNP out of the model was determined at the p<0.001 level. A total of 118 SNPs were detected; 15, 20, 22, 28, 20, and 13 SNPs for final weight before slaughter, carcass weight, backfat thickness, weight index, longissimus dorsi muscle area, and marbling score, respectively. Among the significant SNPs, the best set of 44 SNPs was determined by stepwise regression procedures with 7, 9, 6, 9, 7, and 6 SNPs for the respective traits. Each set of SNPs per trait explained 20-40% of phenotypic variance. The number of detected SNPs per trait was not great in whole genome association tests, suggesting additional phenotype and genotype data are required to get more power to detect the trait-related SNPs with high accuracy for estimation of the SNP effect. These SNP markers could be applied to commercial Hanwoo populations via marker-assisted selection to verify the SNP effects and to improve genetic potentials in successive generations of the Hanwoo populations.

The Effects of Bee Venom and Melittin on NO, iNOS and MAP Kinase Family in RAW 264.7Cellscells (봉양침액(蜂藥鍼液)과 melittin이 RAW 264.7세포(細胞)의 NO, iNOS 및 MAPK에 미치는 영향(影響))

  • Kang, Jun;Song, Ho-sueb
    • Journal of Acupuncture Research
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    • v.21 no.3
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    • pp.107-119
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    • 2004
  • Objective : The purpose of this study was to investigate the effect of Bee Venom and melittin on the lipopolysaccharide(LPS) and sodium nitroprusside(SNP)-induced expressions of Cell viability, nitric oxide(NO), inducible nitric oxide synthase(iNOS), extra-signal response kinase(ERK), jun N-terminal Kinase(JNK) and p38 kinase(p38)- mitogen activated protein kinase(MAPK) Family- in RAW 264.7 cells, a murine macrophage cell line. Methods : The expressions of cell viability by MTT assay, NO by Nitrite assay and iNOS, ERK, JNK and p38 were determined by Western blotting. Results : 1. Compared with the control group, 0.5, 1, $5{\mu}g/m{\ell}$ bee venom and 5, $10{\mu}g/m{\ell}$ melittin increased cell viability of RAW 264.7 induced by LPS and SNP significantly respectively. 2. Compared with the control group, 0.5, 1, $5{\mu}g/m{\ell}$ bee venom and 5, $10{\mu}g/m{\ell}$ melittin inhibited expression of NO induced by LPS and SNP significantly respectively. 3. Compared with the control group, 1, $5{\mu}g/m{\ell}$ bee venom and 5, $10{\mu}g/m{\ell}$ melittin inhibited expression of iNOS induced by LPS significantly and 0.5, 1, $5{\mu}g/m{\ell}$ bee venom and 5, $10{\mu}g/m{\ell}$ melittin inhibited expression of iNOS induced by SNP significantly. 4. Compared with the control group, the expression of ERK induced by LPS and SNP decreased significantly in the treatment groups of $5{\mu}g/m{\ell}$ bee venom and 5, $10{\mu}g/m{\ell}$ melittin, which of p-ERK by LPS also did in 1, $5{\mu}g/m{\ell}$ bee venom and 5, $10{\mu}g/m{\ell}$ melittin, but which of p-ERK by SNP did not decrease. 5. Compared with the control group, the. expression of JNK induced by LPS and SNP decreased significantly in the treatment groups of 5, $10{\mu}g/m{\ell}$ melittin, which of p-JNK by LPS in 5, $10{\mu}g/m{\ell}$ melittin and by SNP in $1{\mu}g/m{\ell}$ bee venom and $10{\mu}g/m{\ell}$ melittin decreased significantly. 6. Compared with the control group, the expression of p38 induced by LPS did not have significant difference, which induced by SNP decreased significantly in the treatment groups of 1, $5{\mu}g/m{\ell}$ bee venom and 5, $10{\mu}g/m{\ell}$ melittin. p-p38 induced by LPS decreased significantly in the treatment group of $10{\mu}g/m{\ell}$ of melittin, which induced by SNP also decreased significantly in 0.5, 1, $5{\mu}g/m{\ell}$ bee venom and 5, $10{\mu}g/m{\ell}$ melittin.

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Analysis of SNPs in Bovine CSRP3, APOBEC2 and Caveolin Gene Family (소의 CSRP3, APOBEC2, Caveolin 유전자들의 단일염기다형 분석)

  • Bhuiyan, M.S.A.;Yu, S.L.;Kim, K.S.;Yoon, D.;Park, E.W.;Jeon, J.T.;Lee, J.H.
    • Journal of Animal Science and Technology
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    • v.49 no.6
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    • pp.719-728
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    • 2007
  • The cysteine and glycine rich protein 3 (CSRP3), apolipoprotein B mRNA editing enzyme catalytic polypeptide‐like 2(APOBEC2) and caveolin (CAV) gene family(CAV1, CAV2, CAV3) have been reported to play important roles for carcass and meat quality traits in pig, mouse, human and cattle. As an initial step, we investigated SNPs in these 5 genes among eight different cattle breeds. Eighteen primer pairs were designed from bovine sequence data of NCBI database to amplify the partial gene fragments. Sequencing results revealed 9 SNPs in the coding regions of three caveolin genes, 1 SNP in CSRP3 and 3 SNPs in APOBEC2 gene. All the identified SNPs were confirmed by PCR-RFLP. Also, 9 more intronic SNPs were detected in these genes. However, all identified mutations in the coding region do not change amino acid sequence. Allelic distributions were significantly different for 5 SNPs in CAV2, CAV3, CSRP3 and APOBEC2 genes among the eight different breeds. These results gave some clues about the polymorphisms of these genes among the cattle breeds and will be useful for further searches for identifying association between these SNPs and meat quality traits in cattle.

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

  • Lee, Seung Hwan;Lim, Dajeong;Jang, Gul Won;Cho, Yong Min;Choi, Bong Hwan;Kim, Si Dong;Oh, Sung Jong;Lee, Jun Heon;Yoon, Duhak;Park, Eung Woo;Lee, Hak Kyo;Hong, Seong Koo;Yang, Boh Suk
    • Journal of Animal Science and Technology
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    • v.54 no.5
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    • pp.323-329
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    • 2012
  • Genome-wide association study was performed on data from 266 Hanwoo steers derived from 66 sires using bovine 10K mapping chip in Hanwoo (Korean cattle). SNPs were excluded from the analysis if they failed in over 5% of the genotypes, had median GC scores below 0.6, had GC scores under 0.6 in less than 90% of the samples, deviated in heterozygosity more than 3 standard deviations from the other SNPs and were out of Hardy-Weinberg equilibrium for a cut-off p-value of $1^{-15}$. Unmapped and SNPs on sex chromosomes were also excluded. A total of 4,522 SNPs were included in the analysis. To test an association between SNP and QTL, a single marker regression analysis was implemented in this study. SNP was assumed to be in LD with QTL in close proximity and the effect evaluated was additive effect (QTL allele substitution effect). The number of significant SNP at a threshold of P<0.001 was 3, 5, 5 and 4 loci for live weight at 6, 12, 18 and 24 months, respectively. For live weight at different ages, significant SNP were spread out across chromosome but some of significant SNP (rs29012453 and rs29012456 on BTA24) had shown highly significant effects. As for the distribution of size of SNP effects, few loci for live weight at different age had moderate effects (6~11%) but most of significant loci had small effects (2 to 5% of additive genetic variance) against total additive genetic variance. In conclusion, live weight at different age might be affected by few loci with moderate effect and many loci with small effects across genome in Hanwoo.