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Volumn 15, Issue 6, 2014, Pages

Mapping-by-sequencing accelerates forward genetics in barley

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME P450; VEGETABLE PROTEIN;

EID: 84912126943     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2014-15-6-r78     Document Type: Article
Times cited : (115)

References (80)
  • 1
    • 84899750824 scopus 로고    scopus 로고
    • Natural variations and genome-wide association studies in crop plants
    • Huang X, Han B: Natural variations and genome-wide association studies in crop plants. Annu Rev Plant Biol 2013, 65:531-551.
    • (2013) Annu Rev Plant Biol , vol.65 , pp. 531-551
    • Huang, X.1    Han, B.2
  • 2
    • 84883757684 scopus 로고    scopus 로고
    • The first 50 plant genomes
    • Michael TP, Jackson S: The first 50 plant genomes. Plant Genome 2013, 6:. doi:10.3835/plantgenome2013.03.0001in.
    • (2013) Plant Genome , vol.6
    • Michael, T.P.1    Jackson, S.2
  • 3
    • 79955726394 scopus 로고    scopus 로고
    • Fast-forward genetics enabled by new sequencing technologies
    • Schneeberger K, Weigel D: Fast-forward genetics enabled by new sequencing technologies. Trends Plant Sci 2011, 16:282-288.
    • (2011) Trends Plant Sci , vol.16 , pp. 282-288
    • Schneeberger, K.1    Weigel, D.2
  • 4
    • 0026052189 scopus 로고
    • Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations
    • Michelmore RW, Paran I, Kesseli RV: Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci U S A 1991, 88:9828-9832.
    • (1991) Proc Natl Acad Sci U S A , vol.88 , pp. 9828-9832
    • Michelmore, R.W.1    Paran, I.2    Kesseli, R.V.3
  • 6
    • 84865086989 scopus 로고    scopus 로고
    • SNP-Ratio Mapping (SRM): identifying lethal alleles and mutations in complex genetic backgrounds by next-generation sequencing
    • Lindner H, RaissigMT, Sailer C, Shimosato-Asano H, Bruggmann R, Grossniklaus U: SNP-Ratio Mapping (SRM): identifying lethal alleles and mutations in complex genetic backgrounds by next-generation sequencing. Genetics 2012, 191:1381-1386.
    • (2012) Genetics , vol.191 , pp. 1381-1386
    • Lindner, H.1    Raissig, M.T.2    Sailer, C.3    Shimosato-Asano, H.4    Bruggmann, R.5    Grossniklaus, U.6
  • 7
    • 84867115083 scopus 로고    scopus 로고
    • Fast isogenic mapping-by-sequencing of ethyl methanesulfonate-induced mutant bulks
    • Hartwig B, James GV, Konrad K, Schneeberger K, Turck F: Fast isogenic mapping-by-sequencing of ethyl methanesulfonate-induced mutant bulks. Plant Physiol 2012, 160:591-600.
    • (2012) Plant Physiol , vol.160 , pp. 591-600
    • Hartwig, B.1    James, G.V.2    Konrad, K.3    Schneeberger, K.4    Turck, F.5
  • 13
    • 34250593039 scopus 로고
    • Die Gaterslebener Mutanten der Saatgerste in Beziehung zur Formenmannigfaltigkeit der Art Hordeum vulgare L. III.
    • Scholz F, Lehmann CO: Die Gaterslebener Mutanten der Saatgerste in Beziehung zur Formenmannigfaltigkeit der Art Hordeum vulgare L. III. Die Kulturpflanze 1961, 9:230-272.
    • (1961) Die Kulturpflanze , vol.9 , pp. 230-272
    • Scholz, F.1    Lehmann, C.O.2
  • 14
    • 84979182716 scopus 로고
    • On the mutagenic action of alkanesulfonic esters in barley
    • Ehrenberg L, Lundqvist U, Osterman S, Sparrman B: On the mutagenic action of alkanesulfonic esters in barley. Hereditas 1966, 56:277-305.
    • (1966) Hereditas , vol.56 , pp. 277-305
    • Ehrenberg, L.1    Lundqvist, U.2    Osterman, S.3    Sparrman, B.4
  • 15
    • 84979186386 scopus 로고
    • A proposed system of symbols for the collection of barley mutants at Svalöv
    • Gustafsson Å, Hagberg A, Lundqvist U, Persson G: A proposed system of symbols for the collection of barley mutants at Svalöv. Hereditas 1969, 62:409-414.
    • (1969) Hereditas , vol.62 , pp. 409-414
    • Gustafsson, Å.1    Hagberg, A.2    Lundqvist, U.3    Persson, G.4
  • 18
    • 77049093783 scopus 로고    scopus 로고
    • TILLING in the two-rowed barley cultivar 'Barke' reveals preferred sites of functional diversity in the gene HvHox1
    • Gottwald S, Bauer P, Komatsuda T, Lundqvist U, Stein N: TILLING in the two-rowed barley cultivar 'Barke' reveals preferred sites of functional diversity in the gene HvHox1. BMC Res Notes 2009, 2:258.
    • (2009) BMC Res Notes , vol.2 , pp. 258
    • Gottwald, S.1    Bauer, P.2    Komatsuda, T.3    Lundqvist, U.4    Stein, N.5
  • 19
    • 5144232519 scopus 로고    scopus 로고
    • A structured mutant population for forward and reverse genetics in Barley (Hordeum vulgare L.)
    • Caldwell DG, McCallum N, Shaw P, Muehlbauer GJ, Marshall DF, Waugh R: A structured mutant population for forward and reverse genetics in Barley (Hordeum vulgare L.). Plant J 2004, 40:143-150.
    • (2004) Plant J , vol.40 , pp. 143-150
    • Caldwell, D.G.1    McCallum, N.2    Shaw, P.3    Muehlbauer, G.J.4    Marshall, D.F.5    Waugh, R.6
  • 23
    • 84870265846 scopus 로고    scopus 로고
    • A physical, genetic and functional sequence assembly of the barley genome
    • International Barley Genome Sequencing Consortium T: A physical, genetic and functional sequence assembly of the barley genome. Nature 2012, 491:711-716.
    • (2012) Nature , vol.491 , pp. 711-716
  • 26
    • 0028323180 scopus 로고
    • Spectrum of X-ray-induced mutations in the human hprt gene
    • Nelson SL, Giver CR, Grosovsky AJ: Spectrum of X-ray-induced mutations in the human hprt gene. Carcinogenesis 1994, 15:495-502.
    • (1994) Carcinogenesis , vol.15 , pp. 495-502
    • Nelson, S.L.1    Giver, C.R.2    Grosovsky, A.J.3
  • 31
    • 0036391767 scopus 로고    scopus 로고
    • Heavy-ioninduced mutations in the gpt delta transgenic mouse: comparison of mutation spectra induced by heavy-ion, X-ray, and gamma-ray radiation
    • Masumura K, Kuniya K, Kurobe T, Fukuoka M, Yatagai F, Nohmi T: Heavy-ioninduced mutations in the gpt delta transgenic mouse: comparison of mutation spectra induced by heavy-ion, X-ray, and gamma-ray radiation. Environ Mol Mutagen 2002, 40:207-215.
    • (2002) Environ Mol Mutagen , vol.40 , pp. 207-215
    • Masumura, K.1    Kuniya, K.2    Kurobe, T.3    Fukuoka, M.4    Yatagai, F.5    Nohmi, T.6
  • 32
    • 77953225557 scopus 로고    scopus 로고
    • Identification of a spontaneous frame shift mutation in a nonreference Arabidopsis accession using whole genome sequencing
    • Laitinen RA, Schneeberger K, Jelly NS, Ossowski S, Weigel D: Identification of a spontaneous frame shift mutation in a nonreference Arabidopsis accession using whole genome sequencing. Plant Physiol 2010, 153:652-654.
    • (2010) Plant Physiol , vol.153 , pp. 652-654
    • Laitinen, R.A.1    Schneeberger, K.2    Jelly, N.S.3    Ossowski, S.4    Weigel, D.5
  • 34
    • 84875718115 scopus 로고    scopus 로고
    • The barley UNICULM2 gene resides in a centromeric region and may be associated with signaling and stress responses
    • Okagaki RJ, Cho S, Kruger WM, Xu WW, Heinen S, Muehlbauer GJ: The barley UNICULM2 gene resides in a centromeric region and may be associated with signaling and stress responses. Funct Integr Genomics 2013, 13:33-41.
    • (2013) Funct Integr Genomics , vol.13 , pp. 33-41
    • Okagaki, R.J.1    Cho, S.2    Kruger, W.M.3    Xu, W.W.4    Heinen, S.5    Muehlbauer, G.J.6
  • 35
    • 84860345912 scopus 로고    scopus 로고
    • High resolution mapping of Dense spike-ar (dsp.ar) to the genetic centromere of barley chromosome 7H
    • Shahinnia F, Druka A, Franckowiak J, Morgante M, Waugh R, Stein N: High resolution mapping of Dense spike-ar (dsp.ar) to the genetic centromere of barley chromosome 7H. Theor Appl Genet 2012, 124:373-384.
    • (2012) Theor Appl Genet , vol.124 , pp. 373-384
    • Shahinnia, F.1    Druka, A.2    Franckowiak, J.3    Morgante, M.4    Waugh, R.5    Stein, N.6
  • 37
    • 84857520461 scopus 로고    scopus 로고
    • Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach
    • Poland JA, Brown PJ, Sorrells ME, Jannink JL: Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 2012, 7:e32253.
    • (2012) PLoS One , vol.7
    • Poland, J.A.1    Brown, P.J.2    Sorrells, M.E.3    Jannink, J.L.4
  • 38
    • 84884835056 scopus 로고    scopus 로고
    • Application of genotypingby- sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley
    • Mascher M, Wu S, Amand PS, Stein N, Poland J: Application of genotypingby- sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS One 2013, 8:e76925.
    • (2013) PLoS One , vol.8
    • Mascher, M.1    Wu, S.2    Amand, P.S.3    Stein, N.4    Poland, J.5
  • 39
    • 77956285690 scopus 로고    scopus 로고
    • Illumina sequencing library preparation for highly multiplexed target capture and sequencing
    • pdb prot5448
    • Meyer M, Kircher M: Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc 2010, 2010:pdb prot5448.
    • (2010) Cold Spring Harb Protoc , vol.2010
    • Meyer, M.1    Kircher, M.2
  • 40
    • 77952516353 scopus 로고    scopus 로고
    • Diversification of P450 genes during land plant evolution
    • Mizutani M, Ohta D: Diversification of P450 genes during land plant evolution. Annu Rev Plant Biol 2010, 61:291-315.
    • (2010) Annu Rev Plant Biol , vol.61 , pp. 291-315
    • Mizutani, M.1    Ohta, D.2
  • 41
    • 0034251820 scopus 로고    scopus 로고
    • CYP78A1 preferentially expressed in developing inflorescences of Zea mays encoded a cytochrome P450-dependent lauric acid 12-monooxygenase
    • Imaishi H, Matsuo S, Swai E, Ohkawa H: CYP78A1 preferentially expressed in developing inflorescences of Zea mays encoded a cytochrome P450-dependent lauric acid 12-monooxygenase. Biosci Biotechnol Biochem 2000, 64:1696-1701.
    • (2000) Biosci Biotechnol Biochem , vol.64 , pp. 1696-1701
    • Imaishi, H.1    Matsuo, S.2    Swai, E.3    Ohkawa, H.4
  • 42
    • 66649124943 scopus 로고    scopus 로고
    • Metabolomics for the characterization of cytochromes P450-dependent fatty acid hydroxylation reactions in Arabidopsis
    • Kai K, Hashidzume H, Yoshimura K, Suzuki H, Sakurai N, Shibata D, Ohta D: Metabolomics for the characterization of cytochromes P450-dependent fatty acid hydroxylation reactions in Arabidopsis. Plant Biotechnol 2009, 26:175-182.
    • (2009) Plant Biotechnol , vol.26 , pp. 175-182
    • Kai, K.1    Hashidzume, H.2    Yoshimura, K.3    Suzuki, H.4    Sakurai, N.5    Shibata, D.6    Ohta, D.7
  • 46
    • 84862190456 scopus 로고    scopus 로고
    • Maternal control of seed size by EOD3/CYP78A6 in Arabidopsis thaliana
    • Fang WJ, Wang ZB, Cui RF, Li J, Li YH: Maternal control of seed size by EOD3/CYP78A6 in Arabidopsis thaliana. Plant J 2012, 70:929-939.
    • (2012) Plant J , vol.70 , pp. 929-939
    • Fang, W.J.1    Wang, Z.B.2    Cui, R.F.3    Li, J.4    Li, Y.H.5
  • 49
    • 0000479431 scopus 로고
    • Isolation of plant DNA from fresh tissue
    • Doyle JJ: Isolation of plant DNA from fresh tissue. Focus 1990, 12:13-15.
    • (1990) Focus , vol.12 , pp. 13-15
    • Doyle, J.J.1
  • 50
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows- Wheeler transform
    • Li H, Durbin R: Fast and accurate short read alignment with Burrows- Wheeler transform. Bioinformatics 2009, 25:1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 51
    • 80054915847 scopus 로고    scopus 로고
    • A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data
    • Li H: A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 2011, 27:2987-2993.
    • (2011) Bioinformatics , vol.27 , pp. 2987-2993
    • Li, H.1
  • 52
    • 84912078124 scopus 로고    scopus 로고
    • The R project
    • The R project. [http://www.r-project.org]
  • 54
    • 84912078125 scopus 로고    scopus 로고
    • Anchoring information of barley WGS assemblies
    • Anchoring information of barley WGS assemblies. [ftp://ftpmips. helmholtz-muenchen.de/plants/barley/public_data/anchoring/wgs_anc/WGS_ANC.TXT]
  • 55
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: a flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26:841-842.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 56
    • 84912140409 scopus 로고    scopus 로고
    • GFF file of barley HC genes
    • GFF file of barley HC genes. [ftp://ftpmips.helmholtz-muenchen.de/plants/barley/public_data/genes/barley_HighConf_genes_MIPS_23Mar12_ HumReadDesc.txt]
  • 57
    • 84912140408 scopus 로고    scopus 로고
    • Barley POPSEQ results
    • Barley POPSEQ results. [ftp://ftp.ipk-gatersleben.de/barley-popseq/]
  • 58
    • 84912140407 scopus 로고    scopus 로고
    • Barley gene expression data
    • Barley gene expression data. [ftp://ftpmips.helmholtz-muenchen.de/plants/barley/public_data/expression/]
  • 59
    • 17444447452 scopus 로고    scopus 로고
    • SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development
    • e
    • Thiel T, Kota R, Grosse I, Stein N, Graner A: SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development. Nucleic Acids Res 2004, 32:e5.
    • (2004) Nucleic Acids Res , vol.32 , pp. 5
    • Thiel, T.1    Kota, R.2    Grosse, I.3    Stein, N.4    Graner, A.5
  • 60
    • 0042120989 scopus 로고    scopus 로고
    • PARSESNP: A tool for the analysis of nucleotide polymorphisms
    • Taylor NE, Greene EA: PARSESNP: A tool for the analysis of nucleotide polymorphisms. Nucleic Acids Res 2003, 31:3808-3811.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3808-3811
    • Taylor, N.E.1    Greene, E.A.2
  • 61
    • 84912096937 scopus 로고    scopus 로고
    • CLC bio website
    • CLC bio website. [www.clcbio.com]
  • 64
    • 84891131572 scopus 로고    scopus 로고
    • Kmasker-A Tool for in silico Prediction of Single-Copy FISH Probes for the Large-Genome Species Hordeum vulgare
    • Schmutzer T, Ma L, Pousarebani N, Bull F, Stein N, Houben A, Scholz U: Kmasker-A Tool for in silico Prediction of Single-Copy FISH Probes for the Large-Genome Species Hordeum vulgare. Cytogenet Genome Res 2014, 142:66-78.
    • (2014) Cytogenet Genome Res , vol.142 , pp. 66-78
    • Schmutzer, T.1    Ma, L.2    Pousarebani, N.3    Bull, F.4    Stein, N.5    Houben, A.6    Scholz, U.7
  • 66
    • 84912078123 scopus 로고    scopus 로고
    • Source code of AHRD
    • Source code of AHRD. [https://github.com/groupschoof/AHRD]
  • 68
    • 84874724662 scopus 로고    scopus 로고
    • Update on activities at the Universal Protein Resource (UniProt) in 2013
    • UniProt C: Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res 2013, 41:D43-D47.
    • (2013) Nucleic Acids Res , vol.41 , pp. D43-D47
    • UniProt, C.1
  • 69
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: A DNA sequence assembly program
    • Huang X, Madan A: CAP3: A DNA sequence assembly program. Genome Res 1999, 9:868-877.
    • (1999) Genome Res , vol.9 , pp. 868-877
    • Huang, X.1    Madan, A.2
  • 74
    • 76749150030 scopus 로고    scopus 로고
    • Genome sequencing and analysis of the model grass Brachypodium distachyon
    • International Brachypodium Initiative T: Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 2010, 463:763-768.
    • (2010) Nature , vol.463 , pp. 763-768
  • 77
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011, 28:2731-2739.
    • (2011) Mol Biol Evol , vol.28 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5    Kumar, S.6
  • 78
    • 84876533617 scopus 로고    scopus 로고
    • Building phylogenetic trees from molecular data with MEGA
    • Hall BG: Building phylogenetic trees from molecular data with MEGA. Mol Biol Evol 2013, 30:1229-1235.
    • (2013) Mol Biol Evol , vol.30 , pp. 1229-1235
    • Hall, B.G.1
  • 79
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones DT, Taylor WR, Thornton JM: The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 1992, 8:275-282.
    • (1992) Comput Appl Biosci , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 80
    • 0000461280 scopus 로고
    • Confidence-limits on phylogenies-an approach using the bootstrap
    • Felsenstein J: Confidence-limits on phylogenies-an approach using the bootstrap. Evolution 1985, 39:783-791.
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1


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