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Volumn 7, Issue 7, 2012, Pages

Development of a large snp genotyping array and generation of high-density genetic maps in tomato

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EID: 84863672047     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0040563     Document Type: Article
Times cited : (262)

References (48)
  • 1
    • 0027745893 scopus 로고
    • Map-based cloning of a protein kinase gene conferring disease resistance in tomato
    • Martin GB, Brommonschenkel SH, Chunwongse J, Frary A, Ganal MW, et al. (1993) Map-based cloning of a protein kinase gene conferring disease resistance in tomato. Science 262: 1432-1436.
    • (1993) Science , vol.262 , pp. 1432-1436
    • Martin, G.B.1    Brommonschenkel, S.H.2    Chunwongse, J.3    Frary, A.4    Ganal, M.W.5
  • 2
    • 0028152968 scopus 로고
    • Isolation of the tomato Cf-9 gene for resistance to Cladosporium fulvum by transposon tagging
    • Jones DA, Thomas CM, Hammondkosack KE, Balintkurti PJ, Jones JDG, (1994) Isolation of the tomato Cf-9 gene for resistance to Cladosporium fulvum by transposon tagging. Science 266: 789-793.
    • (1994) Science , vol.266 , pp. 789-793
    • Jones, D.A.1    Thomas, C.M.2    Hammondkosack, K.E.3    Balintkurti, P.J.4    Jones, J.D.G.5
  • 4
    • 0032144421 scopus 로고    scopus 로고
    • The root knot nematode resistance gene Mi from tomato is a member of the leucine zipper, nucleotide binding, leucine-rich repeat family of plant genes
    • Milligan SB, Bodeau J, Yaghoobi J, Kaloshian I, Zabel P, et al. (1998) The root knot nematode resistance gene Mi from tomato is a member of the leucine zipper, nucleotide binding, leucine-rich repeat family of plant genes. Plant Cell 10: 1307-1319.
    • (1998) Plant Cell , vol.10 , pp. 1307-1319
    • Milligan, S.B.1    Bodeau, J.2    Yaghoobi, J.3    Kaloshian, I.4    Zabel, P.5
  • 5
    • 0031835077 scopus 로고    scopus 로고
    • The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristems and is the ortholog of CEN and TFL1
    • Pnueli L, CarmelGoren L, Hareven D, Gutfinger T, Alvarez J, et al. (1998) The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristems and is the ortholog of CEN and TFL1. Development 125: 1979-1989.
    • (1998) Development , vol.125 , pp. 1979-1989
    • Pnueli, L.1    CarmelGoren, L.2    Hareven, D.3    Gutfinger, T.4    Alvarez, J.5
  • 6
    • 40849085290 scopus 로고    scopus 로고
    • A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit
    • Xiao H, Jiang N, Schaffner E, Stockinger EJ, van der Knaap E, (2008) A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319: 1527-1530.
    • (2008) Science , vol.319 , pp. 1527-1530
    • Xiao, H.1    Jiang, N.2    Schaffner, E.3    Stockinger, E.J.4    van der Knaap, E.5
  • 7
    • 0034718562 scopus 로고    scopus 로고
    • An alternative pathway to beta-carotene formation in plant chromoplasts discovered by map-based cloning of Beta and old-gold color mutations in tomato
    • Ronen G, Carmel-Goren L, Zamir D, Hirschberg J, (2000) An alternative pathway to beta-carotene formation in plant chromoplasts discovered by map-based cloning of Beta and old-gold color mutations in tomato. Proc Natl Acad Sci U S A 97: 11102-11107.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 11102-11107
    • Ronen, G.1    Carmel-Goren, L.2    Zamir, D.3    Hirschberg, J.4
  • 9
  • 10
    • 79952837514 scopus 로고    scopus 로고
    • Mapping and linkage disequilibrium analysis with a genome-wide collection of SNPs that detect polymorphism in cultivated tomato
    • Robbins MD, Sim S, Yang W, van Deynze A, van der Knaap E, et al. (2011) Mapping and linkage disequilibrium analysis with a genome-wide collection of SNPs that detect polymorphism in cultivated tomato. Journal of experimental botany 62: 1831-1845.
    • (2011) Journal of Experimental Botany , vol.62 , pp. 1831-1845
    • Robbins, M.D.1    Sim, S.2    Yang, W.3    van Deynze, A.4    van der Knaap, E.5
  • 11
    • 53649106195 scopus 로고    scopus 로고
    • Next-generation DNA sequencing
    • Shendure J, Ji H, (2008) Next-generation DNA sequencing. Nat Biotechnol 26: 1135-1145.
    • (2008) Nat Biotechnol , vol.26 , pp. 1135-1145
    • Shendure, J.1    Ji, H.2
  • 12
    • 77952425335 scopus 로고    scopus 로고
    • Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery
    • Deschamps S, Campbell MA, (2010) Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery. Mol Breed 25: 553-570.
    • (2010) Mol Breed , vol.25 , pp. 553-570
    • Deschamps, S.1    Campbell, M.A.2
  • 14
    • 68149145780 scopus 로고    scopus 로고
    • Genomewide SNP variation reveals relationships among landraces and modern varieties of rice
    • McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, et al. (2009) Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci U S A 106: 12273-12278.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 12273-12278
    • McNally, K.L.1    Childs, K.L.2    Bohnert, R.3    Davidson, R.M.4    Zhao, K.5
  • 15
    • 77951217695 scopus 로고    scopus 로고
    • Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms
    • Yamamoto T, Nagasaki H, Yonemaru J, Ebana K, Nakajima M, et al. (2010) Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. BMC Genomics 11: 267.
    • (2010) BMC Genomics , vol.11 , pp. 267
    • Yamamoto, T.1    Nagasaki, H.2    Yonemaru, J.3    Ebana, K.4    Nakajima, M.5
  • 17
    • 79961173230 scopus 로고    scopus 로고
    • High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.)
    • Trebbi D, Maccaferri M, de Heer P, Sorensen A, Giuliani S, et al. (2011) High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.). Theor Appl Genet 123: 555-569.
    • (2011) Theor Appl Genet , vol.123 , pp. 555-569
    • Trebbi, D.1    Maccaferri, M.2    de Heer, P.3    Sorensen, A.4    Giuliani, S.5
  • 18
    • 64749112341 scopus 로고    scopus 로고
    • Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing
    • Bundock PC, Eliott FG, Ablett G, Benson AD, Casu RE, et al. (2009) Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. Plant Biotechnol J 7: 347-354.
    • (2009) Plant Biotechnol J , vol.7 , pp. 347-354
    • Bundock, P.C.1    Eliott, F.G.2    Ablett, G.3    Benson, A.D.4    Casu, R.E.5
  • 19
    • 76749130701 scopus 로고    scopus 로고
    • High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence
    • Hyten DL, Cannon SB, Song QJ, Weeks N, Fickus EW, et al. (2010) High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence. BMC Genomics 11: 38.
    • (2010) BMC Genomics , vol.11 , pp. 38
    • Hyten, D.L.1    Cannon, S.B.2    Song, Q.J.3    Weeks, N.4    Fickus, E.W.5
  • 20
    • 78650668282 scopus 로고    scopus 로고
    • Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome
    • Kim MY, Lee S, van K, Kim TH, Jeong SC, et al. (2010) Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc Natl Acad Sci U S A 107: 22032-22037.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 22032-22037
    • Kim, M.Y.1    Lee, S.2    van, K.3    Kim, T.H.4    Jeong, S.C.5
  • 21
    • 79958071911 scopus 로고    scopus 로고
    • Single nucleotide polymorphism discovery in elite north american potato germplasm
    • Hamilton JP, Hansey CN, Whitty BR, Stoffel K, Massa AN, et al. (2011) Single nucleotide polymorphism discovery in elite north american potato germplasm. BMC Genomics 12: 12.
    • (2011) BMC Genomics , vol.12 , pp. 12
    • Hamilton, J.P.1    Hansey, C.N.2    Whitty, B.R.3    Stoffel, K.4    Massa, A.N.5
  • 22
    • 84863681911 scopus 로고    scopus 로고
    • Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis
    • Hamilton JP, Sim S, Stoffel K, van Deynze A, Buell CR, et al. (2012) Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis. The Plant Genome 5: 17-29.
    • (2012) The Plant Genome , vol.5 , pp. 17-29
    • Hamilton, J.P.1    Sim, S.2    Stoffel, K.3    van Deynze, A.4    Buell, C.R.5
  • 23
  • 24
    • 45549086886 scopus 로고    scopus 로고
    • Array-based high-throughput DNA markers for crop improvement
    • Gupta PK, Rustgi S, Mir RR, (2008) Array-based high-throughput DNA markers for crop improvement. Heredity 101: 5-18.
    • (2008) Heredity , vol.101 , pp. 5-18
    • Gupta, P.K.1    Rustgi, S.2    Mir, R.R.3
  • 25
    • 82955201636 scopus 로고    scopus 로고
    • A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome
    • Ganal MW, Durstewitz G, Polley A, Berard A, Buckler ES, et al. (2011) A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PLoS ONE 6: e28334.
    • (2011) PLoS ONE , vol.6
    • Ganal, M.W.1    Durstewitz, G.2    Polley, A.3    Berard, A.4    Buckler, E.S.5
  • 27
    • 70449512421 scopus 로고    scopus 로고
    • Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with breeding
    • Sim SC, Robbins MD, Chilcott C, Zhu T, Francis DM, (2009) Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with breeding. BMC Genomics 10: 10.
    • (2009) BMC Genomics , vol.10 , pp. 10
    • Sim, S.C.1    Robbins, M.D.2    Chilcott, C.3    Zhu, T.4    Francis, D.M.5
  • 28
    • 0026623504 scopus 로고
    • Two-dimensional spreads of synaptonemal complexes from solanaceous plants.5. Tomato (Lycopersicon esculentum) karyotype and idiogram
    • Sherman JD, Stack SM, (1992) Two-dimensional spreads of synaptonemal complexes from solanaceous plants.5. Tomato (Lycopersicon esculentum) karyotype and idiogram. Genome 35: 354-359.
    • (1992) Genome , vol.35 , pp. 354-359
    • Sherman, J.D.1    Stack, S.M.2
  • 29
    • 0028846653 scopus 로고
    • An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL
    • Eshed Y, Zamir D, (1995) An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics 141: 1147-1162.
    • (1995) Genetics , vol.141 , pp. 1147-1162
    • Eshed, Y.1    Zamir, D.2
  • 30
    • 84863693752 scopus 로고    scopus 로고
    • The tomato genome sequence provides insights into fleshy fruit evolution
    • The Tomato Genome Consortium
    • The Tomato Genome Consortium, (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485: 635-641.
    • (2012) Nature , vol.485 , pp. 635-641
  • 31
    • 0035984048 scopus 로고    scopus 로고
    • Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants
    • Fulton TM, van der Hoeven R, Eannetta NT, Tanksley SD, (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14: 1457-1467.
    • (2002) Plant Cell , vol.14 , pp. 1457-1467
    • Fulton, T.M.1    van der Hoeven, R.2    Eannetta, N.T.3    Tanksley, S.D.4
  • 32
    • 22844452344 scopus 로고    scopus 로고
    • Development of a set of PCR-based anchor markers encompassing the tomato genome and evaluation of their usefulness for genetics and breeding experiments
    • Frary A, Xu YM, Liu JP, Mitchell S, Tedeschi E, et al. (2005) Development of a set of PCR-based anchor markers encompassing the tomato genome and evaluation of their usefulness for genetics and breeding experiments. Theor Appl Genet 111: 291-312.
    • (2005) Theor Appl Genet , vol.111 , pp. 291-312
    • Frary, A.1    Xu, Y.M.2    Liu, J.P.3    Mitchell, S.4    Tedeschi, E.5
  • 33
    • 0001145125 scopus 로고
    • Expression of unilateral incompatibility in pollen of Lycopersicon pennellii is determined by major loci on chromosomes 1, 6 and 10
    • Chetelat RT, Deverna JW, (1991) Expression of unilateral incompatibility in pollen of Lycopersicon pennellii is determined by major loci on chromosomes 1, 6 and 10. Theor Appl Genet 82: 704-712.
    • (1991) Theor Appl Genet , vol.82 , pp. 704-712
    • Chetelat, R.T.1    Deverna, J.W.2
  • 34
    • 11244249544 scopus 로고    scopus 로고
    • High-resolution fine mapping and fluorescence in situ hybridization analysis of sun, a locus controlling tomato fruit shape, reveals a region of the tomato genome prone to DNA rearrangements
    • van der Knaap E, Sanyal A, Jackson SA, Tanksley SD, (2004) High-resolution fine mapping and fluorescence in situ hybridization analysis of sun, a locus controlling tomato fruit shape, reveals a region of the tomato genome prone to DNA rearrangements. Genetics 168: 2127-2140.
    • (2004) Genetics , vol.168 , pp. 2127-2140
    • van der Knaap, E.1    Sanyal, A.2    Jackson, S.A.3    Tanksley, S.D.4
  • 37
    • 0029933320 scopus 로고    scopus 로고
    • Molecular mapping of the centromeres of tomato chromosomes 7 and 9
    • Frary A, Presting GG, Tanksley SD, (1996) Molecular mapping of the centromeres of tomato chromosomes 7 and 9. Mol Gen Genet 250: 295-304.
    • (1996) Mol Gen Genet , vol.250 , pp. 295-304
    • Frary, A.1    Presting, G.G.2    Tanksley, S.D.3
  • 38
    • 33748700045 scopus 로고    scopus 로고
    • A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits
    • Wenzl P, Li HB, Carling J, Zhou MX, Raman H, et al. (2006) A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits. BMC Genomics 7: 206.
    • (2006) BMC Genomics , vol.7 , pp. 206
    • Wenzl, P.1    Li, H.B.2    Carling, J.3    Zhou, M.X.4    Raman, H.5
  • 39
    • 31744440502 scopus 로고    scopus 로고
    • A unified mixed-model method for association mapping that accounts for multiple levels of relatedness
    • Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, et al. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38: 203-208.
    • (2006) Nat Genet , vol.38 , pp. 203-208
    • Yu, J.1    Pressoir, G.2    Briggs, W.H.3    Vroh Bi, I.4    Yamasaki, M.5
  • 40
    • 0035045051 scopus 로고    scopus 로고
    • Prediction of total genetic value using genome-wide dense marker maps
    • Meuwissen THE, Hayes BJ, Goddard ME, (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819-1829.
    • (2001) Genetics , vol.157 , pp. 1819-1829
    • Meuwissen, T.H.E.1    Hayes, B.J.2    Goddard, M.E.3
  • 41
    • 84863591750 scopus 로고    scopus 로고
    • Accuracy and Training Population Design for Genomic Selection on Quantitative Traits in Elite North American Oats
    • Asoro FG, Newell MA, Beavis WD, Scott MP, Jannink JL, (2011) Accuracy and Training Population Design for Genomic Selection on Quantitative Traits in Elite North American Oats. The Plant Genome 4: 132-144.
    • (2011) The Plant Genome , vol.4 , pp. 132-144
    • Asoro, F.G.1    Newell, M.A.2    Beavis, W.D.3    Scott, M.P.4    Jannink, J.L.5
  • 42
    • 80053633450 scopus 로고    scopus 로고
    • Genomic Selection Accuracy for Grain Quality Traits in Biparental Wheat Populations
    • Heffner EL, Jannink JL, Iwata H, Souza E, Sorrells ME, (2011) Genomic Selection Accuracy for Grain Quality Traits in Biparental Wheat Populations. Crop Sci 51: 2597-2606.
    • (2011) Crop Sci , vol.51 , pp. 2597-2606
    • Heffner, E.L.1    Jannink, J.L.2    Iwata, H.3    Souza, E.4    Sorrells, M.E.5
  • 43
    • 84861792509 scopus 로고    scopus 로고
    • Accuracy of genomic selection in European maize elite breeding populations
    • Zhao Y, Gowda M, Liu W, Würschum T, Maurer HP, et al. (2012) Accuracy of genomic selection in European maize elite breeding populations. Theor Appl Genet 124: 769-776.
    • (2012) Theor Appl Genet , vol.124 , pp. 769-776
    • Zhao, Y.1    Gowda, M.2    Liu, W.3    Würschum, T.4    Maurer, H.P.5
  • 44
    • 0036320058 scopus 로고    scopus 로고
    • The broad-spectrum potato cyst nematode resistance gene (Hero) from tomato is the only member of a large gene family of NBS-LRR genes with an unusual amino acid repeat in the LRR region
    • Ernst K, Kumar A, Kriseleit D, Kloos DU, Phillips MS, et al. (2002) The broad-spectrum potato cyst nematode resistance gene (Hero) from tomato is the only member of a large gene family of NBS-LRR genes with an unusual amino acid repeat in the LRR region. Plant J 31: 127-136.
    • (2002) Plant J , vol.31 , pp. 127-136
    • Ernst, K.1    Kumar, A.2    Kriseleit, D.3    Kloos, D.U.4    Phillips, M.S.5
  • 45
    • 0036235825 scopus 로고    scopus 로고
    • Two loci from Lycopersicon hirsutum LA407 confer resistance to strains of Clavibacter michiganensis subsp. michiganensis
    • Kabelka E, Franchino B, Francis DM, (2002) Two loci from Lycopersicon hirsutum LA407 confer resistance to strains of Clavibacter michiganensis subsp. michiganensis. Phytopathology 92: 504-510.
    • (2002) Phytopathology , vol.92 , pp. 504-510
    • Kabelka, E.1    Franchino, B.2    Francis, D.M.3
  • 46
    • 34547137178 scopus 로고    scopus 로고
    • JoinMap® 4.0, Software for the calculation of genetic linkage maps in experimental populations
    • van Ooijen JW, (2006) JoinMap® 4.0, Software for the calculation of genetic linkage maps in experimental populations. Kyazma B.V., Wageningen, Netherlands.
    • (2006) Kyazma B.V., Wageningen, Netherlands
    • van Ooijen, J.W.1
  • 47
    • 0035164656 scopus 로고    scopus 로고
    • Map Manager QTX, cross-platform software for genetic mapping
    • Manly KF, Cudmore RH Jr, Meer JM, (2001) Map Manager QTX, cross-platform software for genetic mapping. Mamm Genome 12: 930-932.
    • (2001) Mamm Genome , vol.12 , pp. 930-932
    • Manly, K.F.1    Cudmore Jr., R.H.2    Meer, J.M.3
  • 48
    • 0036256695 scopus 로고    scopus 로고
    • MapChart: software for the graphical presentation of linkage maps and QTLs
    • Voorrips RE, (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93: 77-78.
    • (2002) J Hered , vol.93 , pp. 77-78
    • Voorrips, R.E.1


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