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Metabolomics in Fruit Development

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Molecular Techniques in Crop Improvement

Abstract

Metabolomics aims at the efficient determination of multiple chemical constituents present in a tissue, a cell layer or ideally a single cell. Metabolomics is currently applied in a large number of life science disciplines. Nuclear Magnetic Resonance (NMR) or Gas- and Liquid-Chromatography coupled to Mass Spectrometry (GC-MS and LC-MS) are the most widespread technologies employed in metabolomics assays. Soft fruit, one of the most metabolite-rich plant organs, was from the first to be subjected to metabolomics investigation. The interest in metabolite profiling of soft fruit could be explained by the large repertoire of metabolites belonging to diverse chemical classes that are formed and catabolized during fruit development, starting from the fertilized ovary up to the ripe, mature fruit. Moreover, fruit constitute an essential part of our diet and the breeding to achieve nutrient-rich varieties entails a comprehensive analysis of their metabolite content. Presently, hundreds of substances, including primary and secondary (or specialized) metabolites have been detected in fruit. Metabolomics has been employed also for following metabolism in transgenic plants, mutants and introgression lines populations. The latter experiments allowed the identification of genomic regions associated with metabolic quality traits. So far, most metabolomics assays in fruit have been focused on two species, namely, tomato and strawberry. It is expected that in the following years the use of metabolomics will be expanded to the investigation of numerous other fruit species.

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References

  • Aaby K, Skrede G, Wrolstad RE (2005) Phenolic composition and antioxidant activities in flesh and achenes of strawberries (Fragaria ananassa). J Agric Food Chem 53:4032–4040

    Article  CAS  PubMed  Google Scholar 

  • Aharoni A, DeVos CHR, Verhoeven HA et al. (2002) Nontargeted metabolome analysis by use of fourier transform ion cyclotron mass spectrometry. OMICS 6:217–234

    Article  CAS  PubMed  Google Scholar 

  • Bewley JD, Black M (1994) Seeds: physiology of development and germination, Ed. 2. Plenum, NY

    Google Scholar 

  • Bino RJ, deVos CHR, Lieberman M et al. (2005) The light-hyperresponsive high pigment-2 dg mutation of tomato: alterations in the fruit metabolome. New Phytol 166:427–438

    Article  CAS  PubMed  Google Scholar 

  • Brown SC, Kruppa G, Dasseux JL (2005) Metabolomics applications of FT-ICR mass spectrometry. Mass Spectrom Rev 24:223–31

    Article  CAS  PubMed  Google Scholar 

  • Carrari F, Fernie AR (2006) Metabolic regulation underlying tomato fruit development. J Exp Bot 57:1883–1897

    Article  CAS  PubMed  Google Scholar 

  • Damian D, Orešič M, Verheij E et al. (2007) Applications of a new subspace clustering algorithm (COSA) in medical systems biology. Metabolomics 3:69–77

    Article  CAS  Google Scholar 

  • Dettmer K, Aronov PA, Hammock BD (2007) Mass-spectrometry based metabolomics. Mass Spectrom Rev 26:51–78

    Article  CAS  PubMed  Google Scholar 

  • Dunn WB, Bailey NJC, Johnson HE (2005) Measuring the metabolome: current analytical technologies. Analyst 130:606–625

    Article  CAS  PubMed  Google Scholar 

  • Fait A, Hanhineva K, Beleggia R et al. (2008) Reconfiguration of the achene and receptacle metabolic networks during strawberry fruit development. Plant Physiol 148:730–750

    Article  CAS  PubMed  Google Scholar 

  • Fernie AR, Trthewey RN, Krotzky AJ et al. (2004) Metabolite profiling: from diagnostics to systems biology. Nat Rev 5:1–7

    Article  Google Scholar 

  • Fiehn O, Kopka J, Dörmann P et al. (2000) Metabolite profiling for plant functional genomics. Nat Biotechnol 18:1157–1161

    Article  CAS  PubMed  Google Scholar 

  • Fiehn O, Sumner LW, Rhee SY et al. (2007) Minimum reporting standards for plant biology context information in metabolomic studies. Metabolomics 3:195–201

    Article  CAS  Google Scholar 

  • Fraser PD, Bramley PM (2006) Metabolic profiling and quantification of carotenoids and related isoprenoids in crop plants. In: Saito K, Dixon R, Willmitzer L (eds) Plant metabolomics, Heidelberg, Springer,Germany, pp 229–240

    Chapter  Google Scholar 

  • Fraser PD, Pinto MES, Holloway DE et al. (2000) Application of high-performance liquid chromatography with photodiode array detection to the metabolic profiling of plant isoprenoids. Plant J 24:551–558

    Article  CAS  PubMed  Google Scholar 

  • Fraser PD, Enfissi EMA, Goodfellow M et al. (2007a) Metabolite profiling of plant carotenoids using matrix assisted laser desorption ionization time of flight mass spectrometry. Plant J 49:552–564

    Article  CAS  PubMed  Google Scholar 

  • Fraser PD, Enfissi EMA, Halket JM et al. (2007b) Manipulation of phytoene levels in tomato fruit: effects on isoprenoids, plastids, and intermediary metabolism. Plant Cell 19:3194–3211

    Article  CAS  PubMed  Google Scholar 

  • Fritz JS (2004) Early milestones in the development of ion-exchange chromatography: a personal account. J Chromatogr A 1039:3–12

    Article  CAS  PubMed  Google Scholar 

  • Fulton TM, Bucheli P, Voirol E et al. (2002) Quantitative trait loci (QTL) affecting sugars, organic acids and other biochemical properties possibly contributing to flavour, identified in four advanced backgross populations of tomato. Euphytica 127:163–177

    Article  CAS  Google Scholar 

  • Gillaspy G, Ben-David H, Gruissem W (1993) Fruits: a developmental perspective. Plant Cell 5:1439–1451

    Article  PubMed  Google Scholar 

  • Glinski M, Weckwerth W (2006) The role of mass spectrometry in plant systems biology. Mass Spectrom Rev 25:173–214

    Article  CAS  PubMed  Google Scholar 

  • Giovannoni JJ (2007) Fruit ripening mutants yield insights into ripening control. Curr Opin Plant Biol 10:283–289

    Article  CAS  PubMed  Google Scholar 

  • Giovannoni JJ, Noensie EN, Ruezinsky DM et al. (1995) Molecular genetic analysis of the ripening-inhibitor and non-ripening loci of tomato: A first step in genetic map-based cloning of fruit ripening genes. Mol Gen Genet 248:195–206

    Article  CAS  PubMed  Google Scholar 

  • Halket JM, Waterman D, Przyborowska AM et al. (2005) Chemical derivatization and mass spectral libraries in metabolic profiling by GC/MS and LC/MS/MS. J Exp Bot 56:219–243

    Article  CAS  PubMed  Google Scholar 

  • Hall RD (2005) Plant metabolomics: from holistic hope, to hype, to hot topic. New Phytol 169:453–468

    Article  Google Scholar 

  • Hancock JF (2000) Strawberries. In A Erez (ed) Temperate fruit crops in warm climates. Kluwer Academic, Dordrecht, the Netherlands

    Google Scholar 

  • Hannum SM (2004) Potential impact of strawberries on human health: a review of the science. Crit Rev Food Sci Nutr 44:1–17

    Article  CAS  PubMed  Google Scholar 

  • Hukkanen AT, Kokko HI, Buchala AJ et al. (2007) Benzothiadiazole induces the accumulation of phenolics and improves resistance to powdery mildew in strawberries. J Agric Food Chem 55:1862–1870

    Article  CAS  PubMed  Google Scholar 

  • Iijima Y, Nakamura, Y, Ogata Y et al. (2008) Metabolite annotations based on the integration of mass spectral information. Plant J. 54:949–962

    Google Scholar 

  • Katajamaa M, Orešič M (2005) Processing methods for differential analysis of LC/MS profile data. BMC Bioinformatics 6:179

    Article  PubMed  Google Scholar 

  • Katajamaa M, Orešič M (2007) Data processing for mass spectrometry-based metabolomics. J Chromatogr A 1158:318–328

    Article  CAS  PubMed  Google Scholar 

  • Ketchum REB, Croteau RB (2006) The taxus metabolome and the elucidation of the Taxol biosynthetic pathway in cell suspension cultures. In: Saito K, Dixon R, Willmitzer L (eds) Plant metabolomics, Springer, Heidelberg, Germany, pp 291–308

    Chapter  Google Scholar 

  • Koponen JM, Happonen AM, Mattila PH et al. (2007) Contents of anthocyanins in selected foods consumed in Finland. J Agric Food Chem 55:1612–9

    Article  CAS  PubMed  Google Scholar 

  • Krishnan P, Kruger NJ, Ratcliffe RG (2005) Metabolite fingerprinting and profiling in plants using NMR. J Exp Bot 56:255–265

    Article  CAS  PubMed  Google Scholar 

  • Kähkönen MP, Hopia AI, Heinonen M (2001) Berry phenolics and their antioxidant activity. J Agric Food Chem 49:4076–4082

    Article  PubMed  Google Scholar 

  • Lange BM (2006) Integrative analysis of metabolic networks: from peaks to flux models? Curr Opin Plant Biol 9:220–226

    Article  PubMed  Google Scholar 

  • Lippman ZB, Semel Y, Zamir D (2007) An integrated view of quantitative trait variation using tomato interspecific introgression lines. Curr Opin Genet Dev 17:545–552

    Article  CAS  PubMed  Google Scholar 

  • Mattoo AK, Sobolev AP, Neelam A et al. (2006) Nuclear magnetic resonance spectroscopy-based metabolite profiling of transgenic tomato fruit engineered to accumulate spermidine and spermine reveals enhanced anabolic and nitrogen-carbon interactions. Plant Phys 142:1759–1770

    Article  CAS  Google Scholar 

  • Mintz-Oron S, Mandel T, Rogachev I et al. (2008) Gene expression and metabolism in tomato fruit surface tissues. Plant Phys. 147:823–851

    Article  CAS  Google Scholar 

  • Moco S, Bino RJ, Vorst O et al. (2006) A liquid chromatography–mass-spectrometry-based metabolome database for tomato. Plant Physiol 141:1205–1218

    Article  CAS  PubMed  Google Scholar 

  • Moco S, Capanoglu E, Tikunov Y et al. (2007) Tissue specialization at the metabolite level is perceived during the development of tomato fruit. J Exp Bot 58:4131–4146

    Article  CAS  PubMed  Google Scholar 

  • Moing A, Renauld C, Gaudillere M et al. (2001) Biochemical changes during fruit development of four strawberry cultivars. J Am Soc Hort Sci 126:394–403

    CAS  Google Scholar 

  • Morgenthal K, Weckwerth W, Steuer R (2006) Metabolomic networks in plants: transitions from pattern recognition to biological interpretation. BioSystems 83:108–117

    Article  CAS  PubMed  Google Scholar 

  • Mullen W, Yokota T, Lean MEJ (2003) Analysis of ellagitannins and conjugates of ellagic acid and quercetin in raspberry fruits by LC-MSn. Phytochemistry 64:617–624

    Article  CAS  PubMed  Google Scholar 

  • Neelam A, Cassol T, Mehta RA et al. (2008) A field grown transgenic tomato line expressing higher levels of polyamines reveals legume cover crop mulch-specific perturbations in fruit phenotype at the levels of metabolite profiles, gene expression, and agronomic characteristics. J Exp Bot 59:2337–2346

    Article  Google Scholar 

  • Puupponen-Pimiä R, Nohynek L, Hartmann-Schmidlin S et al. (2005) Berry phenolics selectively inhibit the growth of intestinal pathogens. J Appl Microbiol 98:991–1000

    Article  PubMed  Google Scholar 

  • Robles P, Pelaz S (2005) Flower and fruit development in Arabidopsis thaliana. Int J Dev Biol 49:633–643

    Article  CAS  PubMed  Google Scholar 

  • Roessner U, Luedemann A, Brust D, Fiehn O, Linke T, Willmitzer L, Fernie AR (2001) Metabolic profiling allows comprehensive phenotyping of genetically or environmentally modified plant systems. Plant Cell 13:11–29

    Article  CAS  PubMed  Google Scholar 

  • Roessner-Tunali U, Hegemann B, Lytovchenko A et al. (2003) Metabolic profiling of transgenic tomato plants overexpressing hexokinase reveals that the influence of hexose phophorylation diminishes during fruit development. Plant Physiol 133:84–99

    Article  CAS  PubMed  Google Scholar 

  • Ryan D, Robards K (2006) Metabolomics: the greatest omics of them all? Anal Chem 78:7954–7958

    Article  CAS  PubMed  Google Scholar 

  • Saito K, Dixon R, Willmitzer L (2006) (eds) Plant metabolomics. Springer, Heidelberg, Germany

    Google Scholar 

  • Schauer N, Semel Y, Roessner U et al. (2006) Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nat Biotech 24:447–454

    Article  CAS  Google Scholar 

  • Schauer N, Semel Y, Balbo I et al. (2008) Mode of inheritance of primary metabolic traits in tomato. Plant Cell 20:509–523

    Article  CAS  PubMed  Google Scholar 

  • Seger C, Sturm S (2007) Analytical aspects of plant metabolite profiling platforms: Current standings and future aims. J Proteome Res 6:480–497

    Article  CAS  PubMed  Google Scholar 

  • Shinbo Y, Nakamura Y, Altaf-Ul-Amin M et al. (2006) KNApSAcK: a comprehensive species-metabolite relationship database. In: Saito K, Dixon RA, Willmitzer L (eds) Biotechnology in agriculture and Forestry, vol. 57. Plant metabolomics Springer, Berlin pp.165–181

    Google Scholar 

  • Tikunov Y, Lommen A, deVos CHR et al. (2005) A novel approach for nontargeted data analysis for metabolomics. Large-scale profiling of tomato fruit volatiles. Plant Physiol 139:1125–1137

    Article  CAS  PubMed  Google Scholar 

  • Unger KK (2004) Scientific achievements of Jack Kirkland to the development of HPLC and in particular to HPLC silica packings – a personal perspective. J Chromatogr A 1060:1–7

    CAS  PubMed  Google Scholar 

  • Ward JL, Baker JM, Beale MH (2007) Recent applications of NMR spectroscopy in plant metabolomics. FEBS J 274:1126–1131

    Article  CAS  PubMed  Google Scholar 

  • Werner RA, Rossmann A, Schwartz C et al. (2004) Biosynthesis of gallic acid in Rhus typhina: discrimination between alternative pathways from natural oxygen isotope abundance. Phytochemistry 65:2809–2813

    Article  CAS  PubMed  Google Scholar 

  • Villas-Boas SG, Mas S, Åkesson M et al. (2005) Mass spectrometry in metabolome analysis. Mass Spectrom Rev 24:613–646

    Article  CAS  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. The University of Kuopio, Kuopio, Finland

    Kati Hanhineva

  2. The Weizmann Institute of Science, Rehovot, Israel

    Asaph Aharoni

Authors
  1. Kati Hanhineva
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  2. Asaph Aharoni
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Correspondence to Asaph Aharoni .

Editor information

Editors and Affiliations

  1. Department of Applied Biology, University of Helsinki, Helsinki, Finland

    S. Mohan Jain

  2. Institute (IRRI), Social Sciences Division, International Rice Research, Metro Manila, Philippines

    D.S. Brar

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Hanhineva, K., Aharoni, A. (2010). Metabolomics in Fruit Development. In: Jain, S., Brar, D. (eds) Molecular Techniques in Crop Improvement. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-2967-6_29

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