메뉴 건너뛰기




Volumn 2015, Issue , 2015, Pages

Reduced representation libraries from DNA pools analysed with next generation semiconductor based-sequencing to identify SNPs in extreme and divergent pigs for back fat thickness

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

EID: 84925307954     PISSN: 2314436X     EISSN: 23144378     Source Type: Journal    
DOI: 10.1155/2015/950737     Document Type: Article
Times cited : (14)

References (36)
  • 1
    • 84890211937 scopus 로고    scopus 로고
    • Pigs as a model for biomedical sciences
    • M. F. Rothschild and A. Ruvinsky, Eds., CAB International, Wallingford, UK, 2nd edition
    • K.N. Kuzmuk and L. B. Schook, "Pigs as a model for biomedical sciences," in The Genetics of the Pig, M. F. Rothschild and A. Ruvinsky, Eds., pp. 426-444, CAB International, Wallingford, UK, 2nd edition, 2011.
    • (2011) The Genetics of the Pig , pp. 426-444
    • Kuzmuk, K.N.1    Schook, L.B.2
  • 3
    • 60649101233 scopus 로고    scopus 로고
    • The production of the heavy pig for high quality processed products
    • P. Bosi and V. Russo, "The production of the heavy pig for high quality processed products," Italian Journal of Animal Science, vol. 3, no. 4, pp. 309-321, 2004.
    • (2004) Italian Journal of Animal Science , vol.3 , Issue.4 , pp. 309-321
    • Bosi, P.1    Russo, V.2
  • 4
    • 84910627952 scopus 로고    scopus 로고
    • Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model
    • L. J. Kogelman, S. Cirera, D. V. Zhernakova, M. Fredholm, L. Franke, and H. N. Kadarmideen, "Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model," BMC Medical Genomics, vol. 7, no. 1, article 57, 2014.
    • (2014) BMC Medical Genomics , vol.7 , Issue.1
    • Kogelman, L.J.1    Cirera, S.2    Zhernakova, D.V.3    Fredholm, M.4    Franke, L.5    Kadarmideen, H.N.6
  • 5
    • 84906226347 scopus 로고    scopus 로고
    • Systems genetics of obesity in an F2 pig model by genome-wide association, genetic network, and pathway analyses
    • L. J. A. Kogelman, S. D. Pant, M. Fredholm, and H. N. Kadarmideen, "Systems genetics of obesity in an F2 pig model by genome-wide association, genetic network, and pathway analyses," Frontiers in Genetics, vol. 5, article 214, 2014.
    • (2014) Frontiers in Genetics , vol.5
    • Kogelman, L.J.A.1    Pant, S.D.2    Fredholm, M.3    Kadarmideen, H.N.4
  • 7
    • 77953738733 scopus 로고    scopus 로고
    • The insulin-like growth factor 2 (IGF2) gene intron3-g.3072g>A polymorphism is not the only sus scrofa chromosome 2p mutation affecting meat production and carcass traits in pigs: Evidence from the effects of a cathepsin D (CTSD) gene polymorphism
    • L. Fontanesi, C. Speroni, L. Buttazzoni et al., "The insulin-like growth factor 2 (IGF2) gene intron3-g.3072g>A polymorphism is not the only sus scrofa chromosome 2p mutation affecting meat production and carcass traits in pigs: Evidence from the effects of a cathepsin D (CTSD) gene polymorphism," Journal of Animal Science, vol. 88, no. 7, pp. 2235-2245, 2010.
    • (2010) Journal of Animal Science , vol.88 , Issue.7 , pp. 2235-2245
    • Fontanesi, L.1    Speroni, C.2    Buttazzoni, L.3
  • 8
    • 77749249518 scopus 로고    scopus 로고
    • Confirmed association between a single nucleotide polymorphism in the FTO gene and obesity-related traits in heavy pigs
    • L. Fontanesi, E. Scotti, L. Buttazzoni et al., "Confirmed association between a single nucleotide polymorphism in the FTO gene and obesity-related traits in heavy pigs," Molecular Biology Reports, vol. 37, no. 1, pp. 461-466, 2010.
    • (2010) Molecular Biology Reports , vol.37 , Issue.1 , pp. 461-466
    • Fontanesi, L.1    Scotti, E.2    Buttazzoni, L.3
  • 9
    • 84882622966 scopus 로고    scopus 로고
    • Identification and association analysis of several hundred single nucleotide polymorphisms within candidate genes for back fat thickness in Italian large white pigs using a selective genotyping approach
    • L. Fontanesi, G. Galimberti, D. G. Calò et al., "Identification and association analysis of several hundred single nucleotide polymorphisms within candidate genes for back fat thickness in Italian large white pigs using a selective genotyping approach," Journal of Animal Science, vol. 90, no. 8, pp. 2450-2464, 2012.
    • (2012) Journal of Animal Science , vol.90 , Issue.8 , pp. 2450-2464
    • Fontanesi, L.1    Galimberti, G.2    Calò, D.G.3
  • 10
    • 84884280845 scopus 로고    scopus 로고
    • Association between melanocortin 4 receptor (MC4R) gene haplotypes and carcass and production traits in Italian Large White pigs evaluated with a selective genotyping approach
    • L. Fontanesi, L. Buttazzoni, G. Galimberti, D. G. Calò, E. Scotti, and V. Russo, "Association between melanocortin 4 receptor (MC4R) gene haplotypes and carcass and production traits in Italian Large White pigs evaluated with a selective genotyping approach," Livestock Science, vol. 157, no. 1, pp. 48-56, 2013.
    • (2013) Livestock Science , vol.157 , Issue.1 , pp. 48-56
    • Fontanesi, L.1    Buttazzoni, L.2    Galimberti, G.3    Calò, D.G.4    Scotti, E.5    Russo, V.6
  • 11
    • 68349137618 scopus 로고    scopus 로고
    • Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology
    • A. M. Ramos, R. P. M. A. Crooijmans, N.A. Affara et al., "Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology," PLoS ONE, vol. 4, no. 8, Article ID e6524, 2009.
    • (2009) PLoS ONE , vol.4 , Issue.8
    • Ramos, A.M.1    Crooijmans, R.P.M.A.2    Affara, N.A.3
  • 12
    • 84868694063 scopus 로고    scopus 로고
    • A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes
    • L. Fontanesi, G. Schiavo, G. Galimberti et al., "A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes," BMC Genomics, vol. 13, no. 1, article 583, 2012.
    • (2012) BMC Genomics , vol.13 , Issue.1
    • Fontanesi, L.1    Schiavo, G.2    Galimberti, G.3
  • 13
    • 84869003221 scopus 로고    scopus 로고
    • Analyses of pig genomes provide insight into porcine demography and evolution
    • M. A. M. Groenen, A. L. Archibald, H. Uenishi et al., "Analyses of pig genomes provide insight into porcine demography and evolution," Nature, vol. 491, no. 7424, pp. 393-398, 2012.
    • (2012) Nature , vol.491 , Issue.7424 , pp. 393-398
    • Groenen, M.A.M.1    Archibald, A.L.2    Uenishi, H.3
  • 14
    • 84904497026 scopus 로고    scopus 로고
    • Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression
    • M. Bosse, H.-J. Megens, L. A. F. Frantz et al., "Genomic analysis reveals selection for Asian genes in European pigs following human-mediated introgression," Nature Communication, vol. 5, article 4392, 2014.
    • (2014) Nature Communication , vol.5
    • Bosse, M.1    Megens, H.-J.2    Frantz, L.A.F.3
  • 15
    • 79960597679 scopus 로고    scopus 로고
    • An integrated semiconductor device enabling non-optical genome sequencing
    • J. M. Rothberg, W. Hinz, T. M. Rearick et al., "An integrated semiconductor device enabling non-optical genome sequencing," Nature, vol. 475, no. 7356, pp. 348-352, 2011.
    • (2011) Nature , vol.475 , Issue.7356 , pp. 348-352
    • Rothberg, J.M.1    Hinz, W.2    Rearick, T.M.3
  • 16
    • 84897654788 scopus 로고    scopus 로고
    • High-throughput SNP discovery in the rabbit (Oryctolagus cuniculus) genome by nextgeneration semiconductor-based sequencing
    • F. Bertolini, G. Schiavo, E. Scotti et al., "High-throughput SNP discovery in the rabbit (Oryctolagus cuniculus) genome by nextgeneration semiconductor-based sequencing," Animal Genetics, vol. 45, no. 2, pp. 304-307, 2014.
    • (2014) Animal Genetics , vol.45 , Issue.2 , pp. 304-307
    • Bertolini, F.1    Schiavo, G.2    Scotti, E.3
  • 18
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • H. Li and R. Durbin, "Fast and accurate short read alignment with Burrows-Wheeler transform," Bioinformatics, vol. 25, no. 14, pp. 1754-1760, 2009.
    • (2009) Bioinformatics , vol.25 , Issue.14 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 19
    • 79952422304 scopus 로고    scopus 로고
    • Quality control and preprocessing of metagenomic datasets
    • R. Schmieder and R. Edwards, "Quality control and preprocessing of metagenomic datasets," Bioinformatics, vol. 27, no. 6, pp. 863-864, 2011.
    • (2011) Bioinformatics , vol.27 , Issue.6 , pp. 863-864
    • Schmieder, R.1    Edwards, R.2
  • 21
    • 84895449611 scopus 로고    scopus 로고
    • The sequence alignment/Map format and SAMtools
    • H. Li, B. Handsaker, A. Wysoker et al., "The sequence alignment/Map format and SAMtools," Bioinformatics, vol. 27, no. 6, pp. 863-864, 2011.
    • (2011) Bioinformatics , vol.27 , Issue.6 , pp. 863-864
    • Li, H.1    Handsaker, B.2    Wysoker, A.3
  • 22
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence alignment/map (SAM) format and SAMtools
    • H. Li, B. Handsaker, A. Wysoker et al., "The Sequence alignment/map (SAM) format and SAMtools," Bioinformatics, vol. 25, no. 16, pp. 2078-2079, 2009.
    • (2009) Bioinformatics , vol.25 , Issue.16 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3
  • 23
    • 84874505761 scopus 로고    scopus 로고
    • Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs
    • A. Esteve-Codina, Y. Paudel, L. Ferretti et al., "Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs," BMC Genomics, vol. 15, article 148, 2013.
    • (2013) BMC Genomics , vol.15
    • Esteve-Codina, A.1    Paudel, Y.2    Ferretti, L.3
  • 24
    • 84855731050 scopus 로고    scopus 로고
    • Ensembl BioMarts: A hub for data retrieval across taxonomic space
    • R. J. Kinsella, A. Kähäri, S. Haider et al., "Ensembl BioMarts: a hub for data retrieval across taxonomic space," Database, vol. 2011, Article ID bar030, 2011.
    • (2011) Database , vol.2011
    • Kinsella, R.J.1    Kähäri, A.2    Haider, S.3
  • 25
    • 77955405475 scopus 로고    scopus 로고
    • Deriving the consequences of genomic variants with the EnsemblAPI and SNP Effect Predictor
    • Article ID
    • W. McLaren, B. Pritchard, D. Rios, Y. Chen, P. Flicek, and F. Cunningham, "Deriving the consequences of genomic variants with the EnsemblAPI and SNP Effect Predictor," Bioinformatics, vol. 26, no. 16, Article IDbtq330, pp. 2069-2070, 2010.
    • (2010) Bioinformatics , vol.26 , Issue.16 , pp. 2069-2070
    • McLaren, W.1    Pritchard, B.2    Rios, D.3    Chen, Y.4    Flicek, P.5    Cunningham, F.6
  • 26
    • 0035026704 scopus 로고    scopus 로고
    • Predicting deleterious amino acid substitutions
    • P. C. Ng and S. Henikoff, "Predicting deleterious amino acid substitutions," Genome Research, vol. 11, no. 5, pp. 863-874, 2001.
    • (2001) Genome Research , vol.11 , Issue.5 , pp. 863-874
    • Ng, P.C.1    Henikoff, S.2
  • 28
    • 79955483667 scopus 로고    scopus 로고
    • A framework for variation discovery and genotyping using next-generationDNA sequencing data
    • M. A. DePristo, E. Banks, R. Poplin et al., "A framework for variation discovery and genotyping using next-generationDNA sequencing data," Nature Genetics, vol. 43, no. 5, pp. 491-498, 2011.
    • (2011) Nature Genetics , vol.43 , Issue.5 , pp. 491-498
    • Depristo, M.A.1    Banks, E.2    Poplin, R.3
  • 29
    • 0034727107 scopus 로고    scopus 로고
    • An SNPmap of the human genome generated by reduced representation shotgun sequencing
    • D. Altshuler, V. J. Pollara, C. R. Cowles et al., "An SNPmap of the human genome generated by reduced representation shotgun sequencing," Nature, vol. 407, no. 6803, pp. 513-516, 2000.
    • (2000) Nature , vol.407 , Issue.6803 , pp. 513-516
    • Altshuler, D.1    Pollara, V.J.2    Cowles, C.R.3
  • 30
    • 40149098690 scopus 로고    scopus 로고
    • SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries
    • C. P. Van Tassell, T. P. L. Smith, L. K. Matukumalli et al., "SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries," Nature Methods, vol. 5, no. 3, pp. 247-252, 2008.
    • (2008) Nature Methods , vol.5 , Issue.3 , pp. 247-252
    • Van Tassell, C.P.1    Smith, T.P.L.2    Matukumalli, L.K.3
  • 31
    • 58149327065 scopus 로고    scopus 로고
    • SNP discovery in swine by reduced representation and high throughput pyrosequencing
    • R. T. Wiedmann, T. P. L. Smith, and D. J. Nonneman, "SNP discovery in swine by reduced representation and high throughput pyrosequencing," BMC Genetics, vol. 9, article 81, 2008.
    • (2008) BMC Genetics , vol.9
    • Wiedmann, R.T.1    Smith, T.P.L.2    Nonneman, D.J.3
  • 32
    • 84864910611 scopus 로고    scopus 로고
    • Whole genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo)
    • M. L. Aslam, J.W. M. Bastiaansen, M. G. Elferink et al., "Whole genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo)," BMC Genomics, vol. 13, no. 1, article 391, 2012.
    • (2012) BMC Genomics , vol.13 , Issue.1
    • Aslam, M.L.1    Bastiaansen, J.W.M.2    Elferink, M.G.3
  • 33
    • 84865591846 scopus 로고    scopus 로고
    • A tale of three next generation sequencing platforms: Comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
    • M. A. Quail, M. Smith, P. Coupland et al., "A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers," BMC Genomics, vol. 13, no. 1, article 341, 2012.
    • (2012) BMC Genomics , vol.13 , Issue.1
    • Quail, M.A.1    Smith, M.2    Coupland, P.3
  • 34
    • 84876933570 scopus 로고    scopus 로고
    • Shining a light on dark sequencing: Characterizing errors in Ion Torrent PGM data
    • L. M. Bragg, G. Stone, M. K. Butler, P. Hugenholtz, and G. W. Tyson, "Shining a light on dark sequencing: characterizing errors in Ion Torrent PGM data," PLoS Computational Biology, vol. 9, no. 4, Article IDe1003031, 2013.
    • (2013) PLoS Computational Biology , vol.9 , Issue.4
    • Bragg, L.M.1    Stone, G.2    Butler, M.K.3    Hugenholtz, P.4    Tyson, G.W.5
  • 35
    • 84898618678 scopus 로고    scopus 로고
    • Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication
    • M. Li, S. Tian, C. K. L. Yeung et al., "Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication," Scientific Reports, vol. 4, article 4678, 2014.
    • (2014) Scientific Reports , vol.4
    • Li, M.1    Tian, S.2    Yeung, C.K.L.3
  • 36
    • 84877862924 scopus 로고    scopus 로고
    • Genotyping-by-sequencing (GBS): A novel, efficient and cost-effective genotyping method for cattle using next-generation sequencing
    • M. De Donato, S. O. Peters, S. E. Mitchell, T. Hussain, and I. G. Imumorin, "Genotyping-by-sequencing (GBS): a novel, efficient and cost-effective genotyping method for cattle using next-generation sequencing," PLoS ONE, vol. 8, no. 5, Article ID e62137, 2013.
    • (2013) PLoS ONE , vol.8 , Issue.5
    • De Donato, M.1    Peters, S.O.2    Mitchell, S.E.3    Hussain, T.4    Imumorin, I.G.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.