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Volumn 64, Issue 18, 2013, Pages 5737-5752

Deciphering genetic diversity and inheritance of tomato fruit weight and composition through a systems biology approach

Author keywords

Fruit; metabolome; proteome; systems biology; tomato

Indexed keywords

ENZYME; PROTEOME; VEGETABLE PROTEIN;

EID: 84891498979     PISSN: 00220957     EISSN: 14602431     Source Type: Journal    
DOI: 10.1093/jxb/ert349     Document Type: Article
Times cited : (24)

References (53)
  • 1
    • 84868288762 scopus 로고    scopus 로고
    • Variation revealed by snp genotyping and morphology provides insight into the origin of the tomato
    • Blanca J, Canizares J, Cordero L, Pascual L, Diez MJ, Nuez F. 2012. Variation revealed by SNP genotyping and morphology provides insight into the origin of the tomato. PLoS One 7, e48198
    • (2012) PLoS One , vol.7
    • Blanca, J.1    Canizares, J.2    Cordero, L.3    Pascual, L.4    Diez, M.J.5    Nuez, F.6
  • 2
    • 33845665396 scopus 로고    scopus 로고
    • Integrated analysis of metabolite and transcript levels reveals the metabolic shifts that underlie tomato fruit development and highlight regulatory aspects of metabolic network behavior
    • Carrari F, Baxter C, Usadel B, et al. 2006. Integrated analysis of metabolite and transcript levels reveals the metabolic shifts that underlie tomato fruit development and highlight regulatory aspects of metabolic network behavior. Plant Physiology 142, 1380-1396
    • (2006) Plant Physiology , vol.142 , pp. 1380-1396
    • Carrari, F.1    Baxter, C.2    Usadel, B.3
  • 3
    • 24644503098 scopus 로고    scopus 로고
    • Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research
    • Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M. 2005. Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674-3676
    • (2005) Bioinformatics , vol.21 , pp. 3674-3676
    • Conesa, A.1    Gotz, S.2    Garcia-Gomez, J.M.3    Terol, J.4    Talon, M.5    Robles, M.6
  • 4
    • 67349091678 scopus 로고    scopus 로고
    • Proton nmr quantitative profiling for quality assessment of greenhouse-grown tomato fruit
    • Deborde C, Maucourt M, Baldet P, et al. 2009. Proton NMR quantitative profiling for quality assessment of greenhouse-grown tomato fruit. Metabolomics 52, 183-198
    • (2009) Metabolomics , vol.52 , pp. 183-198
    • Deborde, C.1    Maucourt, M.2    Baldet, P.3
  • 7
    • 84891502169 scopus 로고    scopus 로고
    • Proteomics and metabolomics
    • In: Liedl B, Labate JA, Stommel JR, Slade A, Kole C, eds. Boca Raton, FL: CRC Press Taylor& Francis Group
    • Faurobert M, Iijima Y, Aoki K. 2013. Proteomics and metabolomics. In: Liedl B, Labate JA, Stommel JR, Slade A, Kole C, eds. Genetics, genomics and breeding of tomato. Boca Raton, FL: CRC Press Taylor& Francis Group, 403-421
    • (2013) Genetics, Genomics And Breeding Of Tomato , pp. 403-421
    • Faurobert, M.1    Iijima, Y.2    Aoki, K.3
  • 9
    • 84858746662 scopus 로고    scopus 로고
    • Review of sparse methods in regression and classification with application to chemometrics
    • Filzmoser P, Gschwandtner M, Todorov V. 2012. Review of sparse methods in regression and classification with application to chemometrics. Journal of Chemometrics 263, 42-51
    • (2012) Journal of Chemometrics , vol.263 , pp. 42-51
    • Filzmoser, P.1    Gschwandtner, M.2    Todorov, V.3
  • 10
    • 70449532378 scopus 로고    scopus 로고
    • An integrative genomics approach for deciphering the complex interactions between ascorbate metabolism and fruit growth and composition in tomato
    • Garcia V, Stevens R, Gil L, et al. 2009. An integrative genomics approach for deciphering the complex interactions between ascorbate metabolism and fruit growth and composition in tomato. Comptes Rendus Biologies 332, 1007-1021
    • (2009) Comptes Rendus Biologies , vol.332 , pp. 1007-1021
    • Garcia, V.1    Stevens, R.2    Gil, L.3
  • 11
    • 14744280370 scopus 로고    scopus 로고
    • A robot-based platform to measure multiple enzyme activities in arabidopsis using a set of cycling assays: Comparison of changes of enzyme activities and transcript levels during diurnal cycles and in prolonged darkness
    • Gibon Y, Blaesing OE, Hannemann J, Carillo P, Hohne M, Hendriks JHM, Palacios N, Cross J, Selbig J, Stitt M. 2004. A robot-based platform to measure multiple enzyme activities in Arabidopsis using a set of cycling assays: Comparison of changes of enzyme activities and transcript levels during diurnal cycles and in prolonged darkness. The Plant Cell 16, 3304-3325
    • (2004) The Plant Cell , vol.16 , pp. 3304-3325
    • Gibon, Y.1    Blaesing, O.E.2    Hannemann, J.3    Carillo, P.4    Hohne, M.5    Hendriks, J.H.M.6    Palacios, N.7    Cross, J.8    Selbig, J.9    Stitt, M.10
  • 12
    • 33749120080 scopus 로고    scopus 로고
    • Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes
    • Gibon Y, Usadel B, Blaesing OE, Kamlage B, Hoehne M, Trethewey R, Stitt M. 2006. Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes. Genome Biology 7, R76
    • (2006) Genome Biology , vol.7
    • Gibon, Y.1    Usadel, B.2    Blaesing, O.E.3    Kamlage, B.4    Hoehne, M.5    Trethewey, R.6    Stitt, M.7
  • 14
    • 2942690153 scopus 로고    scopus 로고
    • Genetic regulation of fruit development and ripening
    • Giovannoni JJ. 2004. Genetic regulation of fruit development and ripening. The Plant Cell 16, S170-S180
    • (2004) The Plant Cell , vol.16
    • Giovannoni, J.J.1
  • 15
    • 77957847679 scopus 로고    scopus 로고
    • Metabolite profiling and quantification of phenolic compounds in methanol extracts of tomato fruit
    • Gomez-Romero M, Segura-Carretero A, Fernandez-Gutierrez A. 2010. Metabolite profiling and quantification of phenolic compounds in methanol extracts of tomato fruit. Phytochemistry 71, 1848-1864
    • (2010) Phytochemistry , vol.71 , pp. 1848-1864
    • Gomez-Romero, M.1    Segura-Carretero, A.2    Fernandez-Gutierrez, A.3
  • 16
    • 42449106989 scopus 로고    scopus 로고
    • Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene cca1
    • Gutierez RA, Stokes TL, Thum K, et al. 2008. Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1. Proceedings of the National Academy of Sciences, USA 105, 4939-4944
    • (2008) Proceedings of the National Academy of Sciences, USA , vol.105 , pp. 4939-4944
    • Gutierez, R.A.1    Stokes, T.L.2    Thum, K.3
  • 19
    • 52449092583 scopus 로고    scopus 로고
    • Integrative analyses of genetic variation in enzyme activities of primary carbohydrate metabolism reveal distinct modes of regulation in arabidopsis thaliana
    • Keurentjes, JJB, Sulpice R, Gibon Y, Steinhauser MC, Fu J, Koornneef M, Stitt M, Vreugdenhil D. 2008. Integrative analyses of genetic variation in enzyme activities of primary carbohydrate metabolism reveal distinct modes of regulation in Arabidopsis thaliana. Genome Biology 9, R129
    • (2008) Genome Biology , vol.9
    • Keurentjes, J.J.B.1    Sulpice, R.2    Gibon, Y.3    Steinhauser, M.C.4    Fu, J.5    Koornneef, M.6    Stitt, M.7    Vreugdenhil, D.8
  • 20
    • 62349101060 scopus 로고    scopus 로고
    • Genetical metabolomics: Closing in on phenotypes
    • Keurentjes JJB. 2009. Genetical metabolomics: Closing in on phenotypes. Current Opinion in Plant Biology 12, 223-230
    • (2009) Current Opinion in Plant Biology , vol.12 , pp. 223-230
    • Keurentjes, J.J.B.1
  • 21
    • 69949161748 scopus 로고    scopus 로고
    • Advancing genetic theory and application by metabolic quantitative trait loci analysis
    • Kliebenstein DJ. 2009a. Advancing genetic theory and application by metabolic quantitative trait loci analysis. The Plant Cell 21, 1637-1646
    • (2009) The Plant Cell , vol.21 , pp. 1637-1646
    • Kliebenstein, D.J.1
  • 22
    • 73949102041 scopus 로고    scopus 로고
    • Quantification of variation in expression networks
    • Kliebenstein DJ. 2009b. Quantification of variation in expression networks. Methods in Molecular Biology 553, 227-245
    • (2009) Methods in Molecular Biology , vol.553 , pp. 227-245
    • Kliebenstein, D.J.1
  • 23
    • 75949084606 scopus 로고    scopus 로고
    • Systems biology uncovers the foundation of natural genetic diversity
    • Kliebenstein DJ. 2010. Systems biology uncovers the foundation of natural genetic diversity. Plant Physiology 152, 480-486
    • (2010) Plant Physiology , vol.152 , pp. 480-486
    • Kliebenstein, D.J.1
  • 24
    • 70350694448 scopus 로고    scopus 로고
    • Integromics: An r package to unravel relationships between two omics datasets
    • Le Cao KA, Gonzalez I, Dejean S. 2009. integrOmics: An R package to unravel relationships between two omics datasets. Bioinformatics 25, 2855-2856
    • (2009) Bioinformatics , vol.25 , pp. 2855-2856
    • Le Cao, K.A.1    Gonzalez, I.2    Dejean, S.3
  • 25
    • 59449093971 scopus 로고    scopus 로고
    • Dominance, overdominance and epistasis condition the heterosis in two heterotic rice hybrids
    • Li L, Lu K, Chen Z, Mu T, Hu Z, Li X. 2008. Dominance, overdominance and epistasis condition the heterosis in two heterotic rice hybrids. Genetics 180, 1725-1742
    • (2008) Genetics , vol.180 , pp. 1725-1742
    • Li, L.1    Lu, K.2    Chen, Z.3    Mu, T.4    Hu, Z.5    Li, X.6
  • 26
  • 27
    • 84865573461 scopus 로고    scopus 로고
    • Patterns and processes in crop domestication: An historical review and quantitative analysis of 203 global food crops
    • Meyer RS, DuVal AE, Jensen HR. 2012. Patterns and processes in crop domestication: An historical review and quantitative analysis of 203 global food crops. New Phytologist 196, 29-48
    • (2012) New Phytologist , vol.196 , pp. 29-48
    • Meyer, R.S.1    DuVal, A.E.2    Jensen, H.R.3
  • 28
    • 0001214694 scopus 로고
    • Rflp analysis of phylogeneticrelationships and genetic-variation in the genus lycopersicon
    • Miller JC, Tanksley SD. 1990. RFLP analysis of phylogeneticrelationships and genetic-variation in the genus Lycopersicon. Theoretical and Applied Genetics 80, 437-448
    • (1990) Theoretical and Applied Genetics , vol.80 , pp. 437-448
    • Miller, J.C.1    Tanksley, S.D.2
  • 29
    • 33845547967 scopus 로고    scopus 로고
    • Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus
    • Morcuende R, Bari R, Gibon Y, et al. 2007. Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus. Plant, Cell and Environment 30, 85-112
    • (2007) Plant, Cell and Environment , vol.30 , pp. 85-112
    • Morcuende, R.1    Bari, R.2    Gibon, Y.3
  • 30
    • 63549110574 scopus 로고    scopus 로고
    • Gene and metabolite regulatory network analysis of early developing fruit tissues highlights new candidate genes for the control of tomato fruit composition and development
    • Mounet F, Moing A, Garcia V, et al. 2009. Gene and metabolite regulatory network analysis of early developing fruit tissues highlights new candidate genes for the control of tomato fruit composition and development. Plant Physiology 149, 1505-1528
    • (2009) Plant Physiology , vol.149 , pp. 1505-1528
    • Mounet, F.1    Moing, A.2    Garcia, V.3
  • 31
    • 0036743506 scopus 로고    scopus 로고
    • Comparative sequencing in the genus lycopersicon: Implications for the evolution of fruit size in the domestication of cultivated tomatoes
    • Nesbitt, TC, Tanksley SD. 2002. Comparative sequencing in the genus Lycopersicon: Implications for the evolution of fruit size in the domestication of cultivated tomatoes. Genetics 162, 365-379
    • (2002) Genetics , vol.162 , pp. 365-379
    • Nesbitt, T.C.1    Tanksley, S.D.2
  • 32
    • 80052398971 scopus 로고    scopus 로고
    • Systems biology of tomato fruit development: Combined transcript, protein, and metabolite analysis of tomato transcription factor nor, rin and ethylene receptor nr mutants reveals novel regulatory interactions
    • Osorio S, Alba R, Damasceno CMB, et al. 2011. Systems biology of tomato fruit development: Combined transcript, protein, and metabolite analysis of tomato transcription factor nor, rin and ethylene receptor nr mutants reveals novel regulatory interactions. Plant Physiology 157, 405-425
    • (2011) Plant Physiology , vol.157 , pp. 405-425
    • Osorio, S.1    Alba, R.2    Damasceno, C.M.B.3
  • 33
    • 33846412959 scopus 로고    scopus 로고
    • Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived arabidopsis seedlings
    • Osuna D, Usadel B, Morcuende R, et al., 2007. Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings. The Plant Journal 49, 463-491
    • (2007) The Plant Journal , vol.49 , pp. 463-491
    • Osuna, D.1    Usadel, B.2    Morcuende, R.3
  • 35
    • 62549164807 scopus 로고    scopus 로고
    • A clarified position for Solanum lycopersicum var cerasiforme in the evolutionary history of tomatoes (solanaceae
    • Ranc N, Munos S, Santoni S, Causse M. 2008. A clarified position for Solanum lycopersicum var. cerasiforme in the evolutionary history of tomatoes (solanaceae). BMC Plant Biology 8, 130
    • (2008) BMC Plant Biology , vol.8 , pp. 130
    • Ranc, N.1    Munos, S.2    Santoni, S.3    Causse, M.4
  • 37
    • 0036428761 scopus 로고    scopus 로고
    • Negative autoregulation speeds the response times of transcription networks
    • Rosenfeld N, Elowitz MB, Alon U. 2002. Negative autoregulation speeds the response times of transcription networks. Journal of Molecular Biology 323, 785-793
    • (2002) Journal of Molecular Biology , vol.323 , pp. 785-793
    • Rosenfeld, N.1    Elowitz, M.B.2    Alon, U.3
  • 38
    • 77951880802 scopus 로고    scopus 로고
    • Metabolomics for functional genomics, systems biology, and biotechnology
    • Saito K, Matsuda F. 2010 Metabolomics for functional genomics, systems biology, and biotechnology. Annual Review of Plant Biology 61, 463-489
    • (2010) Annual Review of Plant Biology , vol.61 , pp. 463-489
    • Saito, K.1    Matsuda, F.2
  • 40
    • 33645746673 scopus 로고    scopus 로고
    • Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement
    • Schauer N, Semel Y, Roessner U, et al. 2006. Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nature Biotechnology 24, 447-454
    • (2006) Nature Biotechnology , vol.24 , pp. 447-454
    • Schauer, N.1    Semel, Y.2    Roessner, U.3
  • 41
    • 84863672047 scopus 로고    scopus 로고
    • Development of a large snp genotyping array and generation of high-density genetic maps in tomato
    • Sim SC, Durstewitz G, Plieske J, et al. 2012. Development of a large SNP genotyping array and generation of high-density genetic maps in tomato. PLoS One 7, e40563
    • (2012) PLoS One , vol.7
    • Sim, S.C.1    Durstewitz, G.2    Plieske, J.3
  • 42
    • 35348906821 scopus 로고    scopus 로고
    • Allele-specific expression patterns reveal biases and embryo-specific parent-of-origin effects in hybrid maize
    • Springer NM, Stupar RM. 2007. Allele-specific expression patterns reveal biases and embryo-specific parent-of-origin effects in hybrid maize. The Plant Cell 19, 2391-2402
    • (2007) The Plant Cell , vol.19 , pp. 2391-2402
    • Springer, N.M.1    Stupar, R.M.2
  • 43
    • 34249847958 scopus 로고    scopus 로고
    • Pcamethods-A bioconductor package providing pca methods for incomplete data
    • Stacklies W, Redestig H, Scholz M, Walther D, Selbig J. 2007. pcaMethods-A bioconductor package providing PCA methods for incomplete data. Bioinformatics 23, 1164-1167
    • (2007) Bioinformatics , vol.23 , pp. 1164-1167
    • Stacklies, W.1    Redestig, H.2    Scholz, M.3    Walther, D.4    Selbig, J.5
  • 46
    • 34249812680 scopus 로고    scopus 로고
    • Candidate genes and quantitative trait loci affecting fruit ascorbic acid content in three tomato populations
    • Stevens R, Buret M, Duffe P, Garchery C, Baldet P, Rothan C, Causse M. 2007. Candidate genes and quantitative trait loci affecting fruit ascorbic acid content in three tomato populations. Plant Physiology 143, 1943-1953
    • (2007) Plant Physiology , vol.143 , pp. 1943-1953
    • Stevens, R.1    Buret, M.2    Duffe, P.3    Garchery, C.4    Baldet, P.5    Rothan, C.6    Causse, M.7
  • 48
    • 0000659678 scopus 로고    scopus 로고
    • Heterosis in plant breeding
    • Oxford: John Wiley & Sons, Inc
    • Stuber CW. 2010. Heterosis in plant breeding. Plant Breeding Reviews 12. Oxford: John Wiley & Sons, Inc
    • (2010) Plant Breeding Reviews , vol.12
    • Stuber, C.W.1
  • 49
    • 84863693752 scopus 로고    scopus 로고
    • The tomato genome sequence provides insights into fleshy fruit evolution
    • Tomato Genome Consortium
    • 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
  • 50
    • 0141451882 scopus 로고    scopus 로고
    • Differential display analysis of gene expression in the cytoplasm of giant cells induced in tomato roots by meloidogyne javanica
    • Wang Z, Potter RH, Jones MG. 2003. Differential display analysis of gene expression in the cytoplasm of giant cells induced in tomato roots by Meloidogyne javanica. Molecular Plant Pathology 4, 361-371
    • (2003) Molecular Plant Pathology , vol.4 , pp. 361-371
    • Wang, Z.1    Potter, R.H.2    Jones, M.G.3
  • 51
    • 67650107787 scopus 로고    scopus 로고
    • Regulatory features underlying pollination-dependent and-independent tomato fruit set revealed by transcript and primary metabolite profiling
    • Wang H, Schauer N, Usadel B, Frasse P, Zouine M, Hernould M, Latche A, Pech JC, Fernie AR, Bouzayen M. 2009. Regulatory features underlying pollination-dependent and-independent tomato fruit set revealed by transcript and primary metabolite profiling. The Plant Cell 21, 1428-1452
    • (2009) The Plant Cell , vol.21 , pp. 1428-1452
    • Wang, H.1    Schauer, N.2    Usadel, B.3    Frasse, P.4    Zouine, M.5    Hernould, M.6    Latche, A.7    Pech, J.C.8    Fernie, A.R.9    Bouzayen, M.10


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