annual plant reviews volume 43 (biology of plant metabolomics) || front matter

fm BLBK354-Hall January 18, 2011 7:40 Trim: 234mm×156mm Series: APR Char Count=

ANNUAL PLANT REVIEWSVOLUME 43

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DEDICATION

I would like to dedicate this book to the memory of my mother, Sally Hall,who as a primary school teacher and an avid lover of nature instilled in me,at a very early age, her particular interest in wild and garden plants. Oneof my earliest memories as a child was when we were once walking in thewoods on our farm and she gave me a wood sorrel leaf (Oxalis acetosella) toeat. I marvelled at the pleasant acidity. But she then also gave me a cloverleaf (Trifolium pretense) to eat, both to emphasize how things that look similarcan actually be inherently (and unpleasantly) very different and also as awarning that I should not eat anything I was not totally sure of. This was myfirst sensory metabolomics experiment, at the age of 3, and my fascinationfor plants has never ebbed since.

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ANNUAL PLANT REVIEWSVOLUME 43Biology of Plant Metabolomics

Edited by

Robert D. HallPlant Research International, Wageningen University and ResearchCentre (Wageningen-UR), PO Box 16, 6700 AA Wageningen,The Netherlands;Centre for BioSystems Genomics, PO Box 98, Wageningen,The Netherlands;Netherlands Metabolomics Centre, Einsteinweg 55, 2333 CC Leiden,The Netherlands.

A John Wiley & Sons, Ltd., Publication

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This edition first published 2011 C© 2011 by Blackwell Publishing Ltd.

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Library of Congress Cataloging-in-Publication Data

Biology of plant metabolomics / edited by Robert Hall.p. cm. – (Annual plant reviews ; v. 43)

Includes bibliographical references and index.ISBN 978-1-4051-9954-4 (hardcover : alk. paper) 1. Plants–Metabolism. I. Hall,

Robert D. (Robert David), 1958– II. Series: Annual plant reviews ; v. 43.QK881.B545 2011572′.42–dc22

2010040815

A catalogue record for this book is available from the British Library.

This book is published in the following electronic formats: ePDF (9781444339932);Wiley Online Library (9781444339956); ePub (9781444339949)

Set in 10/12 pt Palatino by Aptara R© Inc., New Delhi, India

1 2011

Cover illustration: The tropical fruit Rambutan (Nephelium lappaceum) is well know for issucculence and exquisite taste. However, as with many plants, as well as providing uswith food, various parts of the plant such as the seeds and bark also provide us with dyes,soaps and medicinals, thus illustrating the huge biochemical diversity that nature offersus. Photo: Robert D. Hall, daily market Luang Prabang, PR Lao.

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Annual Plant ReviewsA series for researchers and postgraduates in the plant sciences. Each volumein this series focuses on a theme of topical importance and emphasis is placedon rapid publication.

Editorial Board:Prof. Jeremy A. Roberts (Editor-in-Chief), Plant Science Division, School of

Biosciences, University of Nottingham, Sutton Bonington Campus,Loughborough, Leicestershire, LE12 5RD, UK;

Dr David Evans, School of Biological and Molecular Sciences, OxfordBrookes University, Headington, Oxford, OX3 0BP;

Dr Michael T. McManus, Institute of Molecular BioSciences, MasseyUniversity, Palmerston North, New Zealand;

Dr Jocelyn K.C. Rose, Department of Plant Biology, Cornell University,Ithaca, New York 14853, USA.

Titles in the series:1. Arabidopsis

Edited by M. Anderson and J.A. Roberts2. Biochemistry of Plant Secondary Metabolism

Edited by M. Wink3. Functions of Plant Secondary Metabolites and their Exploitation in

BiotechnologyEdited by M. Wink

4. Molecular Plant PathologyEdited by M. Dickinson and J. Beynon

5. Vacuolar CompartmentsEdited by D.G. Robinson and J.C. Rogers

6. Plant ReproductionEdited by S.D. O’Neill and J.A. Roberts

7. Protein–Protein Interactions in Plant BiologyEdited by M.T. McManus, W.A. Laing, and A.C. Allan

8. The Plant CellWallEdited by J.K.C. Rose

9. The Golgi Apparatus and the Plant Secretory PathwayEdited by D.G. Robinson

10. The Plant Cytoskeleton in Cell Differentiation and DevelopmentEdited by P.J. Hussey

11. Plant–Pathogen InteractionsEdited by N.J. Talbot

12. Polarity in PlantsEdited by K. Lindsey

13. PlastidsEdited by S.G. Moller

14. Plant Pigments and their ManipulationEdited by K.M. Davies

15. Membrane Transport in PlantsEdited by M.R. Blatt

16. Intercellular Communication in PlantsEdited by A.J. Fleming


17. Plant Architecture and Its ManipulationEdited by C.G.N. Turnbull

18. PlasmodeomataEdited by K.J. Oparka

19. Plant EpigeneticsEdited by P. Meyer

20. Flowering and Its ManipulationEdited by C. Ainsworth

21. Endogenous Plant RhythmsEdited by A. Hall and H. McWatters

22. Control of Primary Metabolism in PlantsEdited by W.C. Plaxton and M.T. McManus

23. Biology of the Plant CuticleEdited by M. Riederer

24. Plant Hormone SignalingEdited by P. Hadden and S.G. Thomas

25. Plant Cell Separation and AdhesionEdited by J.R. Roberts and Z. Gonzalez-Carranza

26. Senescence Processes in PlantsEdited by S. Gan

27. Seed Development, Dormancy and GerminationEdited by K.J. Bradford and H. Nonogaki

28. Plant ProteomicsEdited by C. Finnie

29. Regulation of Transcription in PlantsEdited by K. Grasser

30. Light and Plant DevelopmentEdited by G. Whitelam

31. Plant MitochondriaEdited by D.C. Logan

32. Cell Cycle Control and Plant DevelopmentEdited by D. Inze

33. Intracellular Signaling in PlantsEdited by Z. Yang

34. Molecular Aspects of Plant Disease ResistanceEdited by J. Parker

35. Plant Systems BiologyEdited by G.M. Coruzzi and R.A. Gutierrez

36. The Moss Physcomitrella patensEdited by C.D. Knight, P.-F. Perroud and D.J. Cove

37. Root DevelopmentEdited by T. Beeckman

38. Fruit Development and Seed DispersalEdited by Lars Østergaard

39. Functions and Biotechnology of Plant Secondary MetabolitesEdited by M. Wink

40. Biochemistry of Plant Secondary MetabolismEdited by M. Wink

41. Plant PolysaccharidesEdited by P. Ulvskov

42. Nitrogen Metabolism in Plants in the Post-genomic EraEdited by C. Foyer and H. Zhang

43. Biology of Plant MetabolomicsEdited by R.D. Hall

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CONTENTS

Contributors xvPreface xxiiiAcknowledgements xxv

1 Plant Metabolomics in a Nutshell: Potential and Future Challenges 1Robert D. Hall

1.1 The history and the goals of plant metabolomics 11.2 The technologies 4

1.2.1 Extraction, separation and detection 61.2.2 Data generation, storage, processing and mining 7

1.3 The applications 101.3.1 Metabolomics and fundamental plant research 111.3.2 Metabolomics and applied plant research 13

1.4 The bottlenecks, the potential and future challenges 151.4.1 Current limitations 161.4.2 Future potential 181.4.3 Challenges for the future 19

Acknowledgements 20References 20

2 Metabolite Analysis and Metabolomics in the Study ofBiotrophic Interactions between Plants and Microbes 25John Draper, Susanne Rasmussen and Hassan Zubair

2.1 Introduction 262.2 Biotrophic phases of interactions between fungal

pathogens and plant hosts 282.2.1 Hemi-biotrophic interactions between

Magnaporthe grisea and grass hosts 292.2.2 Infection of cereal hosts by the obligate

pathogen Blumeria graminis 332.2.3 Interactions between maize and smut

pathogen Ustilago maydis 342.3 Mutualistic plant associations with endosymbionts 36

2.3.1 Legume – rhizobium associations 372.3.2 Plant root – arbuscular mycorrhizal associations 402.3.3 Neotyphodium – grass associations 43

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viii � Contents

2.4 Conclusions, horizon scanning & future impact 452.4.1 Common aspects of biotrophic interactions

derived from metabolite analyses 462.4.2 Technical challenges remaining in the study

of biotrophic interactions 47References 49

3 Abiotic Stress and Metabolomics 61Jairus Bowne, Antony Bacic, Mark Tester and Ute Roessner

3.1 Introduction 613.2 What is abiotic stress and how does it impact crop

production? 633.3 Abiotic stress adaptation and tolerance mechanisms:

molecular and physiological approaches 643.4 Metabolomics 65

3.4.1 Gas chromatography–mass spectrometry 663.4.2 Liquid chromatography–mass spectrometry 683.4.3 Capillary electrophoresis–mass spectrometry 693.4.4 Nuclear magnetic resonance 69

3.5 Impact of abiotic stress on plant metabolism 703.5.1 Drought 713.5.2 Cold stress 723.5.3 Salinity 73

3.6 Integration of ‘omics and physiological data 743.7 How can technological improvements assist in data

interpretation? 753.8 Where do we go from here? 76

References 77

4 A Role for Metabolomics in Plant Ecology 87Nicole M. van Dam and Eddy van der Meijden

4.1 A plant is never alone 884.2 Applying metabolomics to wild plant species: yes

we can! 894.3 Plant metabolomics and chemical ecology of

plant–insect interactions: some success stories 924.3.1 The chemical consequences of hybridization

in plants 924.3.2 The search for resistance traits 934.3.3 Genotype x environment interactions in

plant chemistry 944.4 Plant metabolomics helps to advance theories in plant

insect interactions 96


Contents � ix

4.4.1 Optimal defence theories: unravellingdifferent plant defence strategies 96

4.4.2 Testing theories of invasive plant species biology 994.5 Metabolomics for plant ecology in the future:

possibilities and pitfalls 101References 102

5 Metabolomics of a Model Fruit: Tomato 109Ric C.H. de Vos, Robert D. Hall and Annick Moing

5.1 Introduction 1105.1.1 Tomato as a model for fleshy fruit 1105.1.2 Metabolomics techniques in tomato fruit research 1115.1.3 Tomato metabolite databases 118

5.2 A few key examples of the broad relevance of tomatofruit metabolomics 120

5.2.1 Tomato metabolomics and human nutrition 1205.2.2 Metabolomics for quality diagnostics of

tomato fruit and their products 1275.2.3 Genetical metabolomics in tomato 1305.2.4 Tomato metabolomics and functional

genomics studies 1325.3 Predictions for the future 137

5.3.1 High throughput strategies 1375.3.2 Micrometabolomics, metabolite

compartmentation and imaging 1395.3.3 Metabolite identification and databases 1405.3.4 Data integration between metabolomics

platforms and between omics strategies 1425.4 Conclusions 143


6 Metabolomics of Arabidopsis thaliana 157Michael H. Beale and Michael R. Sussman

6.1 Introduction 1576.2 The Arabidopsis metabolome 1596.3 Measuring the Arabidopsis metabolome 162

6.3.1 Technology and methodology 1636.3.2 Putting the technology into practice: targeted

vs. untargeted metabolomics 1666.4 Metabolomics and Arabidopsis molecular plant physiology 1686.5 Metabolomics in Arabidopsis functional genomics 1706.6 Genetical metabolomics 172


x � Contents

6.7 Forward look 173Acknowledgements 174References 174

7 Crops and Tasty, Nutritious Food – How Can Metabolomics Help? 181Derek Stewart, Louise V.T. Shepherd, Robert D. Hall and Paul D.Fraser

7.1 Every food chain begins with plants 1827.2 Potato and tomato – both fresh and processed 182

7.2.1 Potato metabolomics 1837.2.2 Fresh tomatoes 1857.2.3 Tomato puree – a model for the food

processing industry? 1877.3 Grain crops 188

7.3.1 The cereals 1887.3.2 Rice metabolomics 190

7.4 Soft fruit metabolomics 1927.5 Metabolomics and our most important beverages –

coffee, tea and wine 1947.5.1 Coffee metabolomics 1947.5.2 Tea metabolomics 1967.5.3 Grapes and wine 198

7.6 Food product contamination and adulteration 2007.7 Metabolite profiling technologies used to evaluate

crop safety 2017.7.1 The generation and standardization of the

biological material 2017.7.2 Evaluation of novel foodstuffs using targeted

metabolite profiling 2027.7.3 Evaluation of novel foodstuffs using

metabolomic and chemical fingerprinting 2037.7.4 Metabolomics in the development and

evaluation of GM crops 2057.7.5 Non-targeted approaches and detection of

unintended effects 2067.8 The future importance of metabolomics in crop research 206


8 Genetics, Genomics and Metabolomics 219Alisdair R. Fernie and Joost J.B. Keurentjes

8.1 Introduction 2208.2 Genetic understanding of metabolism in the

pre-genomics era 221


Contents � xi

8.2.1 The potential of natural diversity 2218.2.2 From single target to untargeted approaches 225

8.3 Genetic analysis of natural variance in plants – RILsand NILs 226

8.4 Analysis of crop natural variance and broad geneticpopulations 230

8.5 Linking genotypic and phenotypic diversity 2338.6 Finding the mechanisms underlying the QTL 2358.7 Integration of omic data with physiological traits 2388.8 Metabolomics aiding the understanding of

quantitative genetics 2418.9 Perspective of metabolomics assisted breeding 243

8.9.1 Conventional mapping based approaches 2438.9.2 Combining metabolomics and association

mapping 2438.10 Concluding remarks and perspective 244

References 246

9 Data Integration, Metabolic Networks and Systems Biology 261Henning Redestig, Jedrzej Szymanski, Masami Y. Hirai, JoachimSelbig, Lothar Willmitzer, Zoran Nikoloski and Kazuki Saito

9.1 Introduction 2619.2 Combining multiple metabolomics platforms 262

9.2.1 Current applications of multi-platform-basedmetabolomics 263

9.2.2 Our example data set 2649.2.3 Analysis of multi-platform data sets 2659.2.4 Mid-level data fusion 2669.2.5 Low-level data fusion 2709.2.6 Conclusion 274

9.3 Integrating transcriptome and metabolome data 2759.3.1 Emergence of omics in plant physiology 2759.3.2 Integration of omics for systematic

understanding of a whole plant 2769.3.3 Integration of transcriptome and

metabolome data into a single matrix 2769.3.4 Global understanding of physiological

phenomena and gene functionalidentification by relating metabolome totranscriptome 278

9.3.5 Application of public transcriptome data sets 2799.3.6 Visualization of transcriptome and

metabolome data on metabolic map 279


xii � Contents

9.3.7 Multivariate analysis and classification ofgenes and metabolites 280

9.3.8 A wide range of applications of integratedtranscript and metabolite profiling 280

9.3.9 Future perspective 2849.4 Network inference in metabolomics 284

9.4.1 Coverage of metabolic pathways by MS data 2859.4.2 Goals of de novo metabolic network reconstruction 2869.4.3 Relevance networks 2879.4.4 Refining relevance networks 2919.4.5 Bayesian networks 2949.4.6 Summary 297

9.5 Metabolomics: the bridge between constraint-basedand kinetic modelling 298

9.5.1 Plant-specific genome-scale metabolic networks 2999.5.2 Classical flux balance analysis 2999.5.3 Dynamic flux balance analysis 3059.5.4 Challenges and opportunities 306


10 Progress in Chemometrics and Biostatistics for PlantApplications, or: A Good Red Wine is a Bad White Wine 317Joachim Kopka, Dirk Walther, J. William Allwood and RoystonGoodacre

10.1 Introduction 31810.2 A metabolomic association analysis of enological

wine quality 32010.2.1 Study design 32010.2.2 Simple questions are the best: which

metabolites characterize a red compared to awhite wine? 323

10.2.3 Hierarchical cluster analysis and principalcomponent analysis are routine tools: arecommon markers for the qualityclassification of red and white wines to beexpected? 325

10.2.4 Data reduction without loss of relevantinformation is a major challenge: consideringconditional aspects of white wine quality 329

10.2.5 Finding associations: which metabolites bestreflect the enological quality of wine? 333

10.2.6 Finding sample classification rules: whichmetabolites allow best prediction ofenological quality of wine? 336


Contents � xiii

10.3 Conclusion: standard operating procedures formetabolomic data mining 339Acknowledgements 340References 341

11 Spatially Resolved Plant Metabolomics 343Lloyd W. Sumner, Dong Sik Yang, Bennie J. Bench, Bonnie S.Watson, Chao Li and A. Daniel Jones

11.1 Introduction 34411.1.1 Spatially resolved primary metabolism 34411.1.2 Spatially resolved secondary metabolism 346

11.2 Current applications of spatially resolvedmetabolomics in plant biology 34811.2.1 Metabolomics of Medicago truncatula floral organs 34811.2.2 Metabolite profiling of alfalfa trichomes 35411.2.3 Spatially resolved metabolomics of alfalfa

(Medicago sativa) border cells and roots 35611.3 Metabolite imaging 357

11.3.1 Mass spectrometric imaging of trichomes 35811.4 Current challenges and future directions of plant

metabolomics 35811.4.1 Metabolite annotation and depth-of-coverage 35911.4.2 Instrumental sensitivity and dynamic range 36011.4.3 Temporally and spatially resolved metabolomics 360


12 Data Processing, Metabolomic Databases and Pathway Analysis 367Oliver Fiehn, Tobias Kind and Dinesh Kumar Barupal

12.1 Introduction 36812.2 Data processing and identification of plant metabolites 369

12.2.1 Gas chromatography – mass spectrometry(GC-MS) 371

12.2.2 Direct infusion nanoelectrospray – tandemmass spectrometry 374

12.2.3 Liquid chromatography – tandem massspectrometry 377

12.3 Compound-centric metabolomic databases andgenomic pathway repositories 38012.3.1 Databases linking metabolomic data to

compound information 38212.3.2 Linking compounds to chemical and

biological information 387


xiv � Contents

12.3.3 Reconstructing plant genomic informationtowards enzymes and pathways 391

12.4 Mapping and visualization of metabolomic data tobiochemical pathways 39512.4.1 Pathway maps 39512.4.2 Mapping to metabolic modules 39612.4.3 Network topology and graph layouts 397

12.5 Conclusions 398Websites 399References 399

Index 407Color plate (between pages 262 and 263)


CONTRIBUTORS

J. William AllwoodSchool of ChemistryManchester Interdisciplinary BiocentreUniversity of Manchester131 Princess StreetManchesterM1 7DNUK

Antony BacicSchool of BotanyUniversity of Melbourne3010 VictoriaAustralia

Dinesh Kumar BarupalUC Davis Genome Center451 Health Sci DrDavisCA 95616USA

Michael H. BealeNational Centre for Plant and Microbial MetabolomicsRothamsted ResearchHarpendenHertsAL5 2JQUK

Bennie J. BenchThe Samuel Roberts Noble FoundationPlant Biology DivisionArdmoreOK 73401USA

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xvi � Contributors

Jairus BowneSchool of BotanyThe University of Melbourne3010 VictoriaAustralia

Ric C.H. de VosPlant Research InternationalWageningen University and Research Centre (Wageningen-UR)PO Box 166700 AA WageningenThe NetherlandsandCentre for BioSystems GenomicsPO Box 986700 AB WageningenThe NetherlandsandNetherlands Metabolomics CentreEinsteinweg 552333 CC LeidenThe Netherlands

John DraperInstitute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythSY23 3DAUK

Alisdair R. FernieMax Planck Institute for Molecular Plant PhysiologyAm Muhlenberg 114476 GolmGermany

Oliver FiehnUC Davis Genome Center451 Health Sci DrDavis CA 95616USA

Paul D. FraserSchool of Biological SciencesRoyal Holloway University of London


Contributors � xvii

EghamSurreyTW20 0EXUK

Royston GoodacreSchool of ChemistryManchester Interdisciplinary BiocentreUniversity of Manchester131 Princess StreetManchesterM1 7DNUK

Robert D. HallPlant Research InternationalWageningen University and Research Centre (Wageningen-UR)PO Box 166700 AA WageningenThe NetherlandsandCentre for BioSystems GenomicsPO Box 986700 AB WageningenThe NetherlandsandNetherlands Metabolomics CentreEinsteinweg 552333 CC LeidenThe Netherlands

Masami Y. HiraiRIKEN Plant Science CenterYokohama-shi17-2-2 Tsurumi-kuSuehiro-cho230-0045 Japan

A. Daniel JonesDepartment of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMI 48823USA


xviii � Contributors

Joost J.B. KeurentjesLaboratory of GeneticsWageningen UniversityDroevendaalsesteeg 16708 PB WageningenThe NetherlandsandLaboratory of Plant PhysiologyWageningen UniversityDroevendaalsesteeg 16708 PB WageningenThe NetherlandsandCentre for Biosystems GenomicsDroevendaalsesteeg 16708 PB WageningenThe Netherlands

Tobias KindUC Davis Genome Center451 Health Sci DrDavisCA 95616USA

Joachim KopkaMax Planck Institute for Molecular Plant PhysiologyAm Muhlenberg 114476 GolmGermany

Chao LiDepartment of ChemistryMichigan State UniversityEast LansingMI 48823USA

Annick MoingINRAUMR619 Fruit BiologyBP 81F-33140Villenave d’OrnonFrance


Contributors � xix

andMetabolome-Fluxome Facility of Bordeaux Functional Genomics CenterIBVMCentre INRA de BordeauxBP 81F-33140 Villenave d’OrnonFrance

Zoran NikoloskiMax Planck Institute for Molecular Plant PhysiologyAm Muhlenberg 114476 GolmGermany

Susanne RasmussenAgResearchPalmerston North 4442New Zealand

Henning RedestigRIKEN Plant Science CenterYokohama-shi17-2-2 Tsurumi-kuSuehiro-cho230-0045 Japan

Ute RoessnerSchool of BotanyUniversity of Melbourne3010 VictoriaAustralia

Kazuki SaitoRIKEN Plant Science CenterYokohama-shi17-2-2 Tsurumi-kuSuehiro-cho230-0045 Japan

Joachim SelbigMax Planck Institute for Molecular Plant PhysiologyAm Muhlenberg 114476 GolmGermany


xx � Contributors

Louise V.T. ShepherdScottish Crop Research InstitutePlant Products and Food Quality ProgrammeMylnefieldInvergowrie DundeeDD2 5DA ScotlandUK

Derek StewartScottish Crop Research InstitutePlant Products and Food Quality ProgrammeMylnefieldInvergowrie DundeeDD2 5DA ScotlandUK

Lloyd W. SumnerThe Samuel Roberts Noble FoundationPlant Biology DivisionArdmoreOK 73401USA

Michael R. SussmanBiotechnology CenterUniversity of Wisconsin425 Henry MallMadisonWI 53706USA

Jedrzej SzymanskiMax Planck Institute for Molecular Plant PhysiologyAm Muhlenberg 114476 GolmGermany

Mark TesterUniversity of AdelaideWaite CampusGlen Osmond5064 SAAustralia


Contributors � xxi

Nicole M. van DamRadboud University NijmegenInstitute for Water and Wetland Research (IWWR)PO Box 90106500 GL NijmegenThe Netherlands

Eddy van der MeijdenInstitute of Biology LeidenPO Box 95169505 RA LeidenThe Netherlands

Dirk WaltherMax Planck Institute for Molecular Plant PhysiologyAm Muhlenberg 114476 GolmGermany

Bonnie S. WatsonThe Samuel Roberts Noble FoundationPlant Biology DivisionArdmoreOK 73401USA

Lothar WillmitzerMax Planck Institute for Molecular Plant PhysiologyAm Muhlenberg 114476 GolmGermany

Dong Sik YangThe Samuel Roberts Noble FoundationPlant Biology DivisionArdmoreOK 73401USA

Hassan ZubairInstitute of Biological Environmental and Rural SciencesAberystwyth UniversityAberystwythSY23 3DAUK


PREFACE

While I think we can surely say that metabolomics has quickly become es-tablished in a sustainable position in the scientific arena, the technology isnevertheless still very much ‘under development’. This will likely remainso for a significant period of time. This is not because we are failing to getthe technology up to scratch, but rather, because our demands, expectationsand even hopes grow with every new experiment we perform. In plants, inparticular, the broad applicability of the technology, as reflected in the scopeof the chapters in this book, has been the primary driving force in getting thetechnology properly developed and integrated. Many, if not all, plant biolo-gists have seen the potential value of having a holistic and detailed insightinto the chemical composition of the materials we work with – be it at thecellular or whole plant level, or be it related to pure fundamental researchinto the complexity of the molecular organization of plants or to the basis ofthe nutritional value of the foods we eat. By having a better understanding ofhow plant metabolism is altered by genetic or environmental perturbation,how it is dependent upon cell and tissue differentiation, how it contributes tothe daily and seasonal functioning of the plant etc., we will gain a better po-sition regarding how we may control or manipulate this towards improvingcrop fitness or productivity, enhancing yield and plant product quality.

Plant metabolomics is, in concept, dedicated to facilitating the generationof an in-depth chemical analysis of plant materials. Immediately after itsinception, or rather the coining of the term in 1998, the approach was under-standably, highly focused on technology developments. This concerned notonly analytical and hardware improvements but also, and more importantly,developments in automated data generation, storage, processing and min-ing. However, in recent years, this focus has gradually moved more and moretowards the actual biological relevance of the data being generated and howthese data can further our biological understanding of crops and other modelplants. For this reason, the primary focus of the chapters in this volume hasbeen chosen to target specifically this aspect and take us one step, at least,above the technological focus that has gone before. Some of the chapters focuson a single species (e.g. tomato and Arabidopsis), emphasising the extensive-ness of the analyses that have already taken place on individual topics, whileothers target specific biological phenomena such as biotic stress, abiotic stressand the ecology of a plant’s interaction with its environment. Authors havebeen chosen who are at the head of their field and, in most cases, chaptershave been written by two or more leading scientists coming from at least twodifferent laboratories, and usually, even from different countries. In this way,

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xxiv � Preface

the reader should gain a broader overview and opinion of the current addedvalue of the technology and its applications as well as developing a moreaccurate vision for the future on how the technology will impact the waywe proceed with plant science. Undeniably, there will be omissions, and wejointly apologize to all those scientists whose work may have been underex-posed. Inevitably, considering the rapid development of the technology, newtopics of potentially equal or greater importance than those covered here willrapidly emerge. This is always the case when an approach of such broad po-tential relevance and applicability quickly becomes adopted and translatedin myriad new directions. We still have the feeling that we are just at thebeginning and that many, new, exciting developments are in store for thefuture. This book, hopefully, will even stimulate and lead us into developingsome of these new ideas and will bring us a step closer to realising the fullbiological potential of plant metabolomics approaches.

Robert HallPlant Research International

Centre for BioSystems GenomicsNetherlands Metabolomics Centre


ACKNOWLEDGEMENTS

The inspiration for this book arose during my activities as a coordinator of anEU-funded project entitled META-PHOR (http://www.meta-phor.eu). Thisproject (FOOD-CT-2006–036220) involved an intensive interaction between22 technology, biology and industrial partners and helped me greatly advanceand broaden my knowledge as a scientist; I greatly value this experience. I,therefore, kindly acknowledge financial support from the European Commis-sion for this work, and in addition, without the initial financial support fromthe Centre for BioSystems Genomics, the Netherlands Metabolomics Centre(both initiatives under the auspices of the Netherlands Genomics Initiative)and Plant Research International, none of our metabolomics ambitions wouldeven have gotten off the ground.

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annual plant reviews volume 43 (biology of plant metabolomics) || front matter

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