메뉴 건너뛰기




Volumn 7, Issue 10, 2012, Pages

Genome-Wide SNP Discovery from Transcriptome of Four Common Carp Strains

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

EID: 84868102862     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0048140     Document Type: Article
Times cited : (75)

References (42)
  • 1
    • 84877580640 scopus 로고    scopus 로고
    • Cultured Aquatic Species Fact Sheets
    • Cultured Aquatic Species Fact Sheets.
  • 2
    • 41749092549 scopus 로고    scopus 로고
    • Genome evolution trend of common carp (Cyprinus carpio L.) as revealed by the analysis of microsatellite loci in a gynogentic family
    • Zhang Y, Liang L, Jiang P, Li D, Lu C, et al. (2008) Genome evolution trend of common carp (Cyprinus carpio L.) as revealed by the analysis of microsatellite loci in a gynogentic family. J Genet Genomics 35: 97-103.
    • (2008) J Genet Genomics , vol.35 , pp. 97-103
    • Zhang, Y.1    Liang, L.2    Jiang, P.3    Li, D.4    Lu, C.5
  • 3
    • 77954959104 scopus 로고    scopus 로고
    • SNP discovery and development of genetic markers for mapping innate immune response genes in common carp (Cyprinus carpio)
    • Kongchum P, Palti Y, Hallerman EM, Hulata G, David L, (2010) SNP discovery and development of genetic markers for mapping innate immune response genes in common carp (Cyprinus carpio). Fish & Shellfish Immunology 29: 356-361.
    • (2010) Fish & Shellfish Immunology , vol.29 , pp. 356-361
    • Kongchum, P.1    Palti, Y.2    Hallerman, E.M.3    Hulata, G.4    David, L.5
  • 4
    • 34548230410 scopus 로고    scopus 로고
    • Development of novel EST-SSR markers in common carp by data mining from public EST sequences
    • Wang D, Liao X, Cheng L, Yu X, Tong J, (2007) Development of novel EST-SSR markers in common carp by data mining from public EST sequences. Aquaculture 271: 558-574.
    • (2007) Aquaculture , vol.271 , pp. 558-574
    • Wang, D.1    Liao, X.2    Cheng, L.3    Yu, X.4    Tong, J.5
  • 5
    • 28744446042 scopus 로고    scopus 로고
    • Genetic variation analysis within and among six varieties of common carp (Cyprinus carpio L.) in China using microsatellite markers
    • Zhou J, Wu Q, Wang Z, Ye Y, (2004) Genetic variation analysis within and among six varieties of common carp (Cyprinus carpio L.) in China using microsatellite markers. Genetika 40: 1389-1393.
    • (2004) Genetika , vol.40 , pp. 1389-1393
    • Zhou, J.1    Wu, Q.2    Wang, Z.3    Ye, Y.4
  • 6
    • 84864974263 scopus 로고    scopus 로고
    • High Throughput Mining and Characterization of Microsatellites from Common Carp Genome
    • Ji P, Zhang Y, Li C, Zhao Z, Wang J, et al. (2012) High Throughput Mining and Characterization of Microsatellites from Common Carp Genome. International Journal of Molecular Sciences 13: 9798-9807.
    • (2012) International Journal of Molecular Sciences , vol.13 , pp. 9798-9807
    • Ji, P.1    Zhang, Y.2    Li, C.3    Zhao, Z.4    Wang, J.5
  • 7
    • 4344648963 scopus 로고    scopus 로고
    • A genetic linkage map of common carp (Cyprinus carpio L.) And mapping of a locus associated with cold tolerance Aquaculture
    • Sun X, Liang L, (2004) A genetic linkage map of common carp (Cyprinus carpio L.) And mapping of a locus associated with cold tolerance Aquaculture. 238: 8.
    • (2004) , vol.238 , pp. 8
    • Sun, X.1    Liang, L.2
  • 8
    • 77951646629 scopus 로고    scopus 로고
    • A linkage map of common carp (Cyprinus carpio) based on AFLP and microsatellite markers
    • Cheng L, Liu L, Yu X, Wang D, Tong J, (2010) A linkage map of common carp (Cyprinus carpio) based on AFLP and microsatellite markers. Anim Genet 41: 191-198.
    • (2010) Anim Genet , vol.41 , pp. 191-198
    • Cheng, L.1    Liu, L.2    Yu, X.3    Wang, D.4    Tong, J.5
  • 9
    • 80055110828 scopus 로고    scopus 로고
    • Generation of the first BAC-based physical map of the common carp genome
    • Xu P, Wang J, Wang J, Cui R, Li Y, et al. (2011) Generation of the first BAC-based physical map of the common carp genome. BMC Genomics 12: 537.
    • (2011) BMC Genomics , vol.12 , pp. 537
    • Xu, P.1    Wang, J.2    Wang, J.3    Cui, R.4    Li, Y.5
  • 10
    • 79958727257 scopus 로고    scopus 로고
    • Defining Global Gene Expression Changes of the Hypothalamic-Pituitary-Gonadal Axis in Female sGnRH-Antisense Transgenic Common Carp (Cyprinus carpio)
    • Xu J, Huang W, Zhong C, Luo D, Li S, et al. (2011) Defining Global Gene Expression Changes of the Hypothalamic-Pituitary-Gonadal Axis in Female sGnRH-Antisense Transgenic Common Carp (Cyprinus carpio). PLoS ONE 6: e21057.
    • (2011) PLoS ONE , vol.6
    • Xu, J.1    Huang, W.2    Zhong, C.3    Luo, D.4    Li, S.5
  • 12
    • 33947406824 scopus 로고    scopus 로고
    • Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome
    • Christoffels A, Bartfai R, Srinivasan H, Komen H, Orban L, (2006) Comparative genomics in cyprinids: common carp ESTs help the annotation of the zebrafish genome. BMC Bioinformatics 7: S2.
    • (2006) BMC Bioinformatics , vol.7
    • Christoffels, A.1    Bartfai, R.2    Srinivasan, H.3    Komen, H.4    Orban, L.5
  • 13
    • 84856407329 scopus 로고    scopus 로고
    • Identification and Profiling of MicroRNAs from Skeletal Muscle of the Common Carp
    • Yan X, Ding L, Li Y, Zhang X, Liang Y, et al. (2012) Identification and Profiling of MicroRNAs from Skeletal Muscle of the Common Carp. PLoS ONE 7: e30925.
    • (2012) PLoS ONE , vol.7
    • Yan, X.1    Ding, L.2    Li, Y.3    Zhang, X.4    Liang, Y.5
  • 14
    • 79960462494 scopus 로고    scopus 로고
    • Construction and characterization of the BAC library for common carp Cyprinus carpio L. and establishment of microsynteny with zebrafish Danio rerio
    • Li Y, Xu P, Zhao Z, Wang J, Zhang Y, et al. (2011) Construction and characterization of the BAC library for common carp Cyprinus carpio L. and establishment of microsynteny with zebrafish Danio rerio. Mar Biotechnol (NY) 13: 706-712.
    • (2011) Mar Biotechnol (NY) , vol.13 , pp. 706-712
    • Li, Y.1    Xu, P.2    Zhao, Z.3    Wang, J.4    Zhang, Y.5
  • 15
    • 79953854462 scopus 로고    scopus 로고
    • Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences
    • Xu P, Li J, Li Y, Cui R, Wang J, et al. (2011) Genomic insight into the common carp (Cyprinus carpio) genome by sequencing analysis of BAC-end sequences. BMC Genomics 12: 188.
    • (2011) BMC Genomics , vol.12 , pp. 188
    • Xu, P.1    Li, J.2    Li, Y.3    Cui, R.4    Wang, J.5
  • 16
    • 35548938195 scopus 로고    scopus 로고
    • Gene expression analysis of estrogenic compounds in the liver of common carp (Cyprinus carpio) using a custom cDNA microarray
    • Moens LN, van der Ven K, Van Remortel P, Del-Favero J, De Coen WM, (2007) Gene expression analysis of estrogenic compounds in the liver of common carp (Cyprinus carpio) using a custom cDNA microarray. J Biochem Mol Toxicol 21: 299-311.
    • (2007) J Biochem Mol Toxicol , vol.21 , pp. 299-311
    • Moens, L.N.1    van der Ven, K.2    Van Remortel, P.3    Del-Favero, J.4    De Coen, W.M.5
  • 17
    • 81455156315 scopus 로고    scopus 로고
    • Molecular characterization of CART, AgRP, and MC4R genes and their expression with fasting and re-feeding in common carp (Cyprinus carpio)
    • Wan Y, Zhang Y, Ji P, Li Y, Xu P, et al. (2011) Molecular characterization of CART, AgRP, and MC4R genes and their expression with fasting and re-feeding in common carp (Cyprinus carpio). Molecular Biology Reports: 1-9.
    • (2011) Molecular Biology Reports , pp. 1-9
    • Wan, Y.1    Zhang, Y.2    Ji, P.3    Li, Y.4    Xu, P.5
  • 18
    • 81455156313 scopus 로고    scopus 로고
    • Genetic Linkage Mapping and Analysis of Muscle Fiber-Related QTLs in Common Carp (Cyprinus carpio L.)
    • Zhang Y, Xu P, Lu C, Kuang Y, Zhang X, et al. (2010) Genetic Linkage Mapping and Analysis of Muscle Fiber-Related QTLs in Common Carp (Cyprinus carpio L.). Marine Biotechnology: 1-17.
    • (2010) Marine Biotechnology , pp. 1-17
    • Zhang, Y.1    Xu, P.2    Lu, C.3    Kuang, Y.4    Zhang, X.5
  • 19
    • 70449713418 scopus 로고    scopus 로고
    • Studies on quantitative trait loci related to activity of lactate dehydrogenase in common carp (Cyprinus carpio)
    • Mao RX, Liu FJ, Zhang XF, Zhang Y, Cao DC, et al. (2009) Studies on quantitative trait loci related to activity of lactate dehydrogenase in common carp (Cyprinus carpio). Yi Chuan 31: 407-411.
    • (2009) Yi Chuan , vol.31 , pp. 407-411
    • Mao, R.X.1    Liu, F.J.2    Zhang, X.F.3    Zhang, Y.4    Cao, D.C.5
  • 22
    • 65649152280 scopus 로고    scopus 로고
    • Two-stage genome-wide association study identifies integrin beta 5 as having potential role in bull fertility
    • Feugang JM, Kaya A, Page GP, Chen L, Mehta T, et al. (2009) Two-stage genome-wide association study identifies integrin beta 5 as having potential role in bull fertility. BMC Genomics 10: 176.
    • (2009) BMC Genomics , vol.10 , pp. 176
    • Feugang, J.M.1    Kaya, A.2    Page, G.P.3    Chen, L.4    Mehta, T.5
  • 23
    • 77953233453 scopus 로고    scopus 로고
    • Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
    • Atwell S, Huang YS, Vilhjalmsson BJ, Willems G, Horton M, et al. (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465: 627-631.
    • (2010) Nature , vol.465 , pp. 627-631
    • Atwell, S.1    Huang, Y.S.2    Vilhjalmsson, B.J.3    Willems, G.4    Horton, M.5
  • 24
    • 78049332150 scopus 로고    scopus 로고
    • Genome-wide association studies of 14 agronomic traits in rice landraces
    • Huang X, Wei X, Sang T, Zhao Q, Feng Q, et al. (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42: 961-967.
    • (2010) Nat Genet , vol.42 , pp. 961-967
    • Huang, X.1    Wei, X.2    Sang, T.3    Zhao, Q.4    Feng, Q.5
  • 25
    • 79251561130 scopus 로고    scopus 로고
    • Genome-wide association study of leaf architecture in the maize nested association mapping population
    • Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, et al. (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43: 159-162.
    • (2011) Nat Genet , vol.43 , pp. 159-162
    • Tian, F.1    Bradbury, P.J.2    Brown, P.J.3    Hung, H.4    Sun, Q.5
  • 26
    • 79251575784 scopus 로고    scopus 로고
    • Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population
    • Kump KL, Bradbury PJ, Wisser RJ, Buckler ES, Belcher AR, et al. (2011) Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet 43: 163-168.
    • (2011) Nat Genet , vol.43 , pp. 163-168
    • Kump, K.L.1    Bradbury, P.J.2    Wisser, R.J.3    Buckler, E.S.4    Belcher, A.R.5
  • 27
    • 56249091439 scopus 로고    scopus 로고
    • Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds
    • Muir WM, Wong GK, Zhang Y, Wang J, Groenen MA, et al. (2008) Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proc Natl Acad Sci U S A 105: 17312-17317.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 17312-17317
    • Muir, W.M.1    Wong, G.K.2    Zhang, Y.3    Wang, J.4    Groenen, M.A.5
  • 28
    • 77952327442 scopus 로고    scopus 로고
    • A genome-wide association study on androstenone levels in pigs reveals a cluster of candidate genes on chromosome 6
    • Duijvesteijn N, Knol EF, Merks JW, Crooijmans RP, Groenen MA, et al. (2010) A genome-wide association study on androstenone levels in pigs reveals a cluster of candidate genes on chromosome 6. BMC Genet 11: 42.
    • (2010) BMC Genet , vol.11 , pp. 42
    • Duijvesteijn, N.1    Knol, E.F.2    Merks, J.W.3    Crooijmans, R.P.4    Groenen, M.A.5
  • 29
    • 73949140644 scopus 로고    scopus 로고
    • Genome-wide association analysis of canine atopic dermatitis and identification of disease related SNPs
    • Wood SH, Ke X, Nuttall T, McEwan N, Ollier WE, et al. (2009) Genome-wide association analysis of canine atopic dermatitis and identification of disease related SNPs. Immunogenetics 61: 765-772.
    • (2009) Immunogenetics , vol.61 , pp. 765-772
    • Wood, S.H.1    Ke, X.2    Nuttall, T.3    McEwan, N.4    Ollier, W.E.5
  • 30
    • 78651551997 scopus 로고    scopus 로고
    • Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array
    • Liu S, Zhou Z, Lu J, Sun F, Wang S, et al. (2011) Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array. BMC Genomics 12: 53.
    • (2011) BMC Genomics , vol.12 , pp. 53
    • Liu, S.1    Zhou, Z.2    Lu, J.3    Sun, F.4    Wang, S.5
  • 31
    • 67650318160 scopus 로고    scopus 로고
    • Construction of genetic linkage maps and comparative genome analysis of catfish using gene-associated markers
    • Kucuktas H, Wang S, Li P, He C, Xu P, et al. (2009) Construction of genetic linkage maps and comparative genome analysis of catfish using gene-associated markers. Genetics 181: 1649-1660.
    • (2009) Genetics , vol.181 , pp. 1649-1660
    • Kucuktas, H.1    Wang, S.2    Li, P.3    He, C.4    Xu, P.5
  • 32
    • 34447277084 scopus 로고    scopus 로고
    • Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers
    • Quilang J, Wang S, Li P, Abernathy J, Peatman E, et al. (2007) Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers. BMC Genomics 8: 157.
    • (2007) BMC Genomics , vol.8 , pp. 157
    • Quilang, J.1    Wang, S.2    Li, P.3    Abernathy, J.4    Peatman, E.5
  • 33
    • 44449161026 scopus 로고    scopus 로고
    • A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers
    • Moen T, Hayes B, Baranski M, Berg PR, Kjoglum S, et al. (2008) A linkage map of the Atlantic salmon (Salmo salar) based on EST-derived SNP markers. BMC Genomics 9: 223.
    • (2008) BMC Genomics , vol.9 , pp. 223
    • Moen, T.1    Hayes, B.2    Baranski, M.3    Berg, P.R.4    Kjoglum, S.5
  • 34
    • 77951241851 scopus 로고    scopus 로고
    • Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua)
    • Hubert S, Higgins B, Borza T, Bowman S, (2010) Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua). BMC Genomics 11: 191.
    • (2010) BMC Genomics , vol.11 , pp. 191
    • Hubert, S.1    Higgins, B.2    Borza, T.3    Bowman, S.4
  • 35
    • 84864757761 scopus 로고    scopus 로고
    • Quantitative trait locus analysis of standard length, body depth and body thickness in mirror carp (Cyprinus carpio L.)
    • Zheng XH, Kuang YY, Lu CY, Wang XP, Li WS, et al. (2011) Quantitative trait locus analysis of standard length, body depth and body thickness in mirror carp (Cyprinus carpio L.). Yi Chuan 33: 1366-1373.
    • (2011) Yi Chuan , vol.33 , pp. 1366-1373
    • Zheng, X.H.1    Kuang, Y.Y.2    Lu, C.Y.3    Wang, X.P.4    Li, W.S.5
  • 36
    • 71949101266 scopus 로고    scopus 로고
    • Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library
    • Sanchez CC, Smith TP, Wiedmann RT, Vallejo RL, Salem M, et al. (2009) Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. BMC Genomics 10: 559.
    • (2009) BMC Genomics , vol.10 , pp. 559
    • Sanchez, C.C.1    Smith, T.P.2    Wiedmann, R.T.3    Vallejo, R.L.4    Salem, M.5
  • 37
    • 84864377334 scopus 로고    scopus 로고
    • Transcriptomic signatures of attachment, NF-kappaB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection
    • Sun F, Peatman E, Li C, Liu S, Jiang Y, et al. (2012) Transcriptomic signatures of attachment, NF-kappaB suppression and IFN stimulation in the catfish gill following columnaris bacterial infection. Dev Comp Immunol 38(1): 169-180.
    • (2012) Dev Comp Immunol , vol.38 , Issue.1 , pp. 169-180
    • Sun, F.1    Peatman, E.2    Li, C.3    Liu, S.4    Jiang, Y.5
  • 38
    • 84862786822 scopus 로고    scopus 로고
    • RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus
    • Li C, Zhang Y, Wang R, Lu J, Nandi S, et al. (2012) RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus. Fish Shellfish Immunol 32: 816-827.
    • (2012) Fish Shellfish Immunol , vol.32 , pp. 816-827
    • Li, C.1    Zhang, Y.2    Wang, R.3    Lu, J.4    Nandi, S.5
  • 39
    • 84859723401 scopus 로고    scopus 로고
    • Transcriptome analysis of silver carp (Hypophthalmichthys molitrix) by paired-end RNA sequencing
    • Fu B, He S, (2012) Transcriptome analysis of silver carp (Hypophthalmichthys molitrix) by paired-end RNA sequencing. DNA Res 19: 131-142.
    • (2012) DNA Res , vol.19 , pp. 131-142
    • Fu, B.1    He, S.2
  • 40
    • 84869119243 scopus 로고    scopus 로고
    • Identification of Genes Potentially Related to Biomineralization and Immunity by Transcriptome Analysis of Pearl Sac in Pearl Oyster Pinctada martensii
    • DOI: 10.1007/s10126-012-9438-3
    • Zhao X, Wang Q, Jiao Y, Huang R, Deng Y, et al. (2012) Identification of Genes Potentially Related to Biomineralization and Immunity by Transcriptome Analysis of Pearl Sac in Pearl Oyster Pinctada martensii. Mar Biotechnol (NY). DOI: 10.1007/s10126-012-9438-3.
    • (2012) Mar Biotechnol (NY)
    • Zhao, X.1    Wang, Q.2    Jiao, Y.3    Huang, R.4    Deng, Y.5
  • 41
    • 84859715310 scopus 로고    scopus 로고
    • Characterization of common carp transcriptome: sequencing, de novo assembly, annotation and comparative genomics
    • Ji P, Liu G, Xu J, Wang X, Li J, et al. (2012) Characterization of common carp transcriptome: sequencing, de novo assembly, annotation and comparative genomics. PLoS ONE 7: e35152.
    • (2012) PLoS ONE , vol.7
    • Ji, P.1    Liu, G.2    Xu, J.3    Wang, X.4    Li, J.5
  • 42
    • 79952070113 scopus 로고    scopus 로고
    • Validation of single nucleotide polymorphism (SNP) markers from an immune Expressed Sequence Tag (EST) turbot, Scophthalmus maximus, database
    • Vera M, Álvarez-Dios JA, Millán A, Pardo BG, Bouza C, et al. (2011) Validation of single nucleotide polymorphism (SNP) markers from an immune Expressed Sequence Tag (EST) turbot, Scophthalmus maximus, database. Aquaculture 313: 31-41.
    • (2011) Aquaculture , vol.313 , pp. 31-41
    • Vera, M.1    Álvarez-Dios, J.A.2    Millán, A.3    Pardo, B.G.4    Bouza, C.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.