Metabolomics for Plant Improvement: Status and Prospects

Post-genomics era has witnessed the development of cutting-edge technologies that have offered cost-efficient and high-throughput ways for molecular characterization of the function of a cell or organism. Large-scale metabolite profiling assays have allowed researchers to access the global data sets of metabolites and the corresponding metabolic pathways in an unprecedented way. Recent efforts in metabolomics have been directed to improve the quality along with a major focus on yield related traits. Importantly, an integration of metabolomics with other approaches such as quantitative genetics, transcriptomics and genetic modification has established its immense relevance to plant improvement. An effective combination of these modern approaches guides researchers to pinpoint the functional gene(s) and the characterization of massive metabolites, in order to prioritize the candidate genes for downstream analyses and ultimately, offering trait specific markers to improve commercially important traits. This in turn will improve the ability of a plant breeder by allowing him to make more informed decisions. Given this, the present review captures the significant leads gained in the past decade in the field of plant metabolomics accompanied by a brief discussion on the current contribution and the future scope of metabolomics to accelerate plant improvement.

[1]  Y. Sang,et al.  Profiling Membrane Lipids in Plant Stress Responses , 2002, The Journal of Biological Chemistry.

[2]  E. Stockinger,et al.  Increasing ω-3 Desaturase Expression in Tomato Results in Altered Aroma Profile and Enhanced Resistance to Cold Stress1[W][OA] , 2010, Plant Physiology.

[3]  E. Pichersky,et al.  Overexpression of the lemon basil alpha-zingiberene synthase gene increases both mono- and sesquiterpene contents in tomato fruit. , 2008, The Plant journal : for cell and molecular biology.

[4]  L. Ziska,et al.  Predicting the impact of changing CO(2) on crop yields: some thoughts on food. , 2007, The New phytologist.

[5]  A. Fernie,et al.  An update on source-to-sink carbon partitioning in tomato , 2014, Front. Plant Sci..

[6]  P. Prasad,et al.  Wheat leaf lipids during heat stress: I. High day and night temperatures result in major lipid alterations. , 2016, Plant, cell & environment.

[7]  U. Roessner,et al.  Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement , 2006, Nature Biotechnology.

[8]  K. Karamanoli,et al.  Integrated analysis of metabolites and proteins reveal aspects of the tissue-specific function of synthetic cytokinin in kiwifruit development and ripening. , 2016, Journal of proteomics.

[9]  S. Komatsu,et al.  Crop proteomics: Aim at sustainable agriculture of tomorrow , 2007, Proteomics.

[10]  Yingjin Yuan,et al.  Lipidomic analysis reveals differential defense responses of Taxus cuspidata cells to two elicitors, methyl jasmonate and cerium (Ce4+). , 2008, Biochimica et biophysica acta.

[11]  A. Sobolev,et al.  Metabolite Adjustments in Drought Tolerant and Sensitive Soybean Genotypes in Response to Water Stress , 2012, PloS one.

[12]  A. Kushalappa,et al.  Identification and characterization of a fusarium head blight resistance gene TaACT in wheat QTL‐2DL , 2016, Plant biotechnology journal.

[13]  Kenji Akiyama,et al.  AtMetExpress Development: A Phytochemical Atlas of Arabidopsis Development[W][OA] , 2009, Plant Physiology.

[14]  H. Bouwmeester,et al.  Metabolomics in the Rhizosphere: Tapping into Belowground Chemical Communication. , 2016, Trends in plant science.

[15]  F. Gubler,et al.  Control of Abscisic Acid Catabolism and Abscisic Acid Homeostasis Is Important for Reproductive Stage Stress Tolerance in Cereals1[W][OA] , 2011, Plant Physiology.

[16]  A. Nadolska-Orczyk,et al.  Silencing of the HvCKX1 gene decreases the cytokinin oxidase/dehydrogenase level in barley and leads to higher plant productivity. , 2010, Journal of experimental botany.

[17]  C. Crisosto,et al.  Application of abscisic acid (ABA) at veraison advanced red color development and maintained postharvest quality of ‘Crimson Seedless’ grapes , 2007 .

[18]  W. Peacock,et al.  Hormone-regulated defense and stress response networks contribute to heterosis in Arabidopsis F1 hybrids , 2015, Proceedings of the National Academy of Sciences.

[19]  M. Stitt,et al.  Genomic and metabolic prediction of complex heterotic traits in hybrid maize , 2012, Nature Genetics.

[20]  Bingru Huang,et al.  Thermotolerance and antioxidant systems in Agrostis stolonifera: involvement of salicylic acid, abscisic acid, calcium, hydrogen peroxide, and ethylene. , 2004, Journal of plant physiology.

[21]  Young-soon Kim,et al.  Senescence-Induced Serotonin Biosynthesis and Its Role in Delaying Senescence in Rice Leaves1[C][W][OA] , 2009, Plant Physiology.

[22]  Shrinidhi S. Hegde,et al.  A mass spectrometric study for comparative analysis and evaluation of metabolite recovery from plasma by various solvent systems. , 2012, Journal of biomolecular techniques : JBT.

[23]  M. Zanor,et al.  Integrated Analysis of Metabolite and Transcript Levels Reveals the Metabolic Shifts That Underlie Tomato Fruit Development and Highlight Regulatory Aspects of Metabolic Network Behavior1[W] , 2006, Plant Physiology.

[24]  John P Reganold,et al.  Utility of metabolomics toward assessing the metabolic basis of quality traits in apple fruit with an emphasis on antioxidants. , 2012, Journal of agricultural and food chemistry.

[25]  Zhentian Lei,et al.  MET-COFEA: a liquid chromatography/mass spectrometry data processing platform for metabolite compound feature extraction and annotation. , 2014, Analytical chemistry.

[26]  Tingting Dong,et al.  Effects of Elevated CO2 and Temperature on Yield and Fruit Quality of Strawberry (Fragaria × ananassa Duch.) at Two Levels of Nitrogen Application , 2012, PloS one.

[27]  Marcel Kuntz,et al.  Evaluation of Genetically Engineered Crops Using Transcriptomic, Proteomic, and Metabolomic Profiling Techniques , 2011, Plant Physiology.

[28]  J. Metraux,et al.  The cuticle , 2008, Plant signaling & behavior.

[29]  G. Chawla,et al.  Principle, Instrumentation, and Applications of UPLC: A Novel Technique of Liquid Chromatography , 2016 .

[30]  R. Birch,et al.  Transgenic expression of trehalulose synthase results in high concentrations of the sucrose isomer trehalulose in mature stems of field-grown sugarcane. , 2011, Plant biotechnology journal.

[31]  Huiliang Li,et al.  Three R2R3 MYB transcription factor genes from Capsicum annuum showing differential expression during fruit ripening , 2011 .

[32]  J. Vrebalov,et al.  The Tomato MADS-Box Transcription Factor RIPENING INHIBITOR Interacts with Promoters Involved in Numerous Ripening Processes in a COLORLESS NONRIPENING-Dependent Manner1[W][OA] , 2011, Plant Physiology.

[33]  E. Heuvelink Effect of fruit load on dry matter partitioning in tomato , 1997 .

[34]  Alejandro Cifuentes,et al.  Metabolomics of Genetically Modified Crops , 2014, International journal of molecular sciences.

[35]  C. Slupsky,et al.  Metabolomic analysis of citrus infection by 'Candidatus Liberibacter' reveals insight into pathogenicity. , 2012, Journal of proteome research.

[36]  Renate A Weizbauer,et al.  Brassinosteroid control of sex determination in maize , 2011, Proceedings of the National Academy of Sciences.

[37]  O. Paulo,et al.  Molecular candidates for early-stage flower-to-fruit transition in stenospermocarpic table grape (Vitis vinifera L.) inflorescences ascribed by differential transcriptome and metabolome profiles. , 2016, Plant science : an international journal of experimental plant biology.

[38]  Luigi Bavaresco,et al.  Study of Grape Polyphenols by Liquid Chromatography-High-Resolution Mass Spectrometry (UHPLC/QTOF) and Suspect Screening Analysis , 2015, Journal of analytical methods in chemistry.

[39]  H. Nguyen,et al.  RNAi-mediated disruption of squalene synthase improves drought tolerance and yield in rice , 2011, Journal of experimental botany.

[40]  M. Stitt,et al.  Increased C availability at elevated carbon dioxide concentration improves N assimilation in a legume. , 2006, Plant, cell & environment.

[41]  Jie Luo,et al.  Comparative and parallel genome-wide association studies for metabolic and agronomic traits in cereals , 2016, Nature Communications.

[42]  L. Gil,et al.  Cuticle Structure in Relation to Chemical Composition: Re-assessing the Prevailing Model , 2016, Front. Plant Sci..

[43]  Yingtian Xie,et al.  Responses of wheat and rice to factorial combinations of ambient and elevated CO2 and temperature in FACE experiments , 2016, Global change biology.

[44]  A. Fernie,et al.  A Reevaluation of the Key Factors That Influence Tomato Fruit Softening and Integrity1[W][OA] , 2007, Plant Physiology.

[45]  H. Wieser,et al.  Effects of elevated CO2 on grain yield and quality of wheat: results from a 3-year free-air CO2 enrichment experiment. , 2009, Plant biology.

[46]  Yuan-Yue Shen,et al.  Abscisic Acid Plays an Important Role in the Regulation of Strawberry Fruit Ripening1[W][OA] , 2011, Plant Physiology.

[47]  E. Pichersky,et al.  Metabolic engineering of plant volatiles. , 2008, Current opinion in biotechnology.

[48]  D. Jacob,et al.  Metabolomic profiling in tomato reveals diel compositional changes in fruit affected by source–sink relationships , 2015, Journal of experimental botany.

[49]  C. Gardner,et al.  Emerging Avenues for Utilization of Exotic Germplasm. , 2017, Trends in plant science.

[50]  Jie Ren,et al.  Suppression of 9-cis-Epoxycarotenoid Dioxygenase, Which Encodes a Key Enzyme in Abscisic Acid Biosynthesis, Alters Fruit Texture in Transgenic Tomato1[W][OA] , 2012, Plant Physiology.

[51]  Q. Qian,et al.  Cytokinin Oxidase Regulates Rice Grain Production , 2005, Science.

[52]  C. N. Stewart,et al.  Transgenic Plant-Produced Hydrolytic Enzymes and the Potential of Insect Gut-Derived Hydrolases for Biofuels , 2016, Front. Plant Sci..

[53]  Does plant size affect growth responses to water availability at glacial, modern and future CO2 concentrations? , 2016, Ecological Research.

[54]  E. Kok,et al.  Comparison of two GM maize varieties with a near-isogenic non-GM variety using transcriptomics, proteomics and metabolomics. , 2010, Plant biotechnology journal.

[55]  C. Pinheiro,et al.  Effect of drought and rewatering on the metabolism of Lupinus albus organs. , 2004, Journal of plant physiology.

[56]  M. Prasad,et al.  Cadmium toxicity and tolerance in vascular plants , 1995 .

[57]  C. Ward,et al.  Kiwifruit: taking its place in the global fruit bowl. , 2013, Advances in food and nutrition research.

[58]  Q. Shen,et al.  A toolbox of genes, proteins, metabolites and promoters for improving drought tolerance in soybean includes the metabolite coumestrol and stomatal development genes , 2016, BMC Genomics.

[59]  L. Ziska,et al.  Interaction of Elevated Ultraviolet-B Radiation and CO(2) on Productivity and Photosynthetic Characteristics in Wheat, Rice, and Soybean. , 1990, Plant physiology.

[60]  W. Davies,et al.  Long-distance ABA Signaling and Its Relation to Other Signaling Pathways in the Detection of Soil Drying and the Mediation of the Plant’s Response to Drought , 2005, Journal of Plant Growth Regulation.

[61]  Takeo Harada,et al.  Null Mutation of the MdACS3 Gene, Coding for a Ripening-Specific 1-Aminocyclopropane-1-Carboxylate Synthase, Leads to Long Shelf Life in Apple Fruit1[W][OA] , 2009, Plant Physiology.

[62]  D. R. Wagner,et al.  Activation Tagging in Tomato Identifies a Transcriptional Regulator of Anthocyanin Biosynthesis, Modification, and Transport Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.012963. , 2003, The Plant Cell Online.

[63]  J. Moulis Cellular mechanisms of cadmium toxicity related to the homeostasis of essential metals , 2010, Biometals.

[64]  M. Landoni,et al.  A paramutation phenomenon is involved in the genetics of maize low phytic acid1-241 (lpa1-241) trait , 2009, Heredity.

[65]  Gel-based proteomics in plants: time to move on from the tradition , 2015, Front. Plant Sci..

[66]  W. Schwab,et al.  Methyl jasmonate treatment induces changes in fruit ripening by modifying the expression of several ripening genes in Fragaria chiloensis fruit. , 2013, Plant physiology and biochemistry : PPB.

[67]  R. Visser,et al.  Enhancing pterin and para-aminobenzoate content is not sufficient to successfully biofortify potato tubers and Arabidopsis thaliana plants with folate. , 2013, Journal of experimental botany.

[68]  W. Vriezen,et al.  The role of auxin and gibberellin in tomato fruit set. , 2009, Journal of experimental botany.

[69]  L. Samuels,et al.  Plant cuticles shine: advances in wax biosynthesis and export. , 2009, Current opinion in plant biology.

[70]  A. Hanson,et al.  ONE-CARBON METABOLISM IN HIGHER PLANTS. , 2001, Annual review of plant physiology and plant molecular biology.

[71]  M. Zhang,et al.  Ethylene independent induction of lycopene biosynthesis in tomato fruits by jasmonates , 2012, Journal of experimental botany.

[72]  J. Rose,et al.  Fruit cuticle lipid composition during development in tomato ripening mutants. , 2010, Physiologia plantarum.

[73]  J. Bohner,et al.  Cell number, cell size and hormone levels in semi‐isogenic mutants of Lycopersicon pimpinellifolium differing in fruit size , 1988 .

[74]  R. Mitchell,et al.  The effects of increasing CO2 on crop photosynthesis and productivity: a review of field studies , 1991 .

[75]  E. Lewinsohn,et al.  Post-harvest enhancement of aroma in transgenic lisianthus (Eustoma grandiflorum) using the Clarkia breweri benzyl alcohol acetyltransferase (BEAT) gene , 2007 .

[76]  S. Xiao,et al.  Non-targeted metabolomic analysis of orange (Citrus sinensis [L.] Osbeck) wild type and bud mutant fruits by direct analysis in real-time and HPLC-electrospray mass spectrometry , 2013, Metabolomics.

[77]  Xiuxin Deng,et al.  Regulation of cuticle formation during fruit development and ripening in 'Newhall' navel orange (Citrus sinensis Osbeck) revealed by transcriptomic and metabolomic profiling. , 2016, Plant science : an international journal of experimental plant biology.

[78]  D. Linke,et al.  Phosphate availability affects the thylakoid lipid composition and the expression of SQD1, a gene required for sulfolipid biosynthesis in Arabidopsis thaliana. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[79]  K. Sakakibara,et al.  Review: genetically modified plants for the promotion of human health , 2006, Biotechnology Letters.

[80]  Mark Stitt,et al.  Malate Plays a Crucial Role in Starch Metabolism, Ripening, and Soluble Solid Content of Tomato Fruit and Affects Postharvest Softening[W][OA] , 2011, Plant Cell.

[81]  A. Aharoni,et al.  Gain and Loss of Fruit Flavor Compounds Produced by Wild and Cultivated Strawberry Species , 2004, The Plant Cell Online.

[82]  A. Fernie,et al.  GDP-D-mannose 3,5-epimerase (GME) plays a key role at the intersection of ascorbate and non-cellulosic cell-wall biosynthesis in tomato. , 2009, The Plant journal : for cell and molecular biology.

[83]  M. Zanor,et al.  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 Interactions1[W][OA] , 2011, Plant Physiology.

[84]  P. Reich,et al.  Carbon-Nitrogen Interactions in Terrestrial Ecosystems in Response to Rising Atmospheric Carbon Dioxide , 2006 .

[85]  L. Willmitzer,et al.  Differential remodeling of the lipidome during cold acclimation in natural accessions of Arabidopsis thaliana. , 2012, The Plant journal : for cell and molecular biology.

[86]  Q. Shen,et al.  Understanding Water-Stress Responses in Soybean Using Hydroponics System—A Systems Biology Perspective , 2015, Front. Plant Sci..

[87]  Alisdair R. Fernie,et al.  Review: Metabolome characterisation in plant system analysis. , 2003, Functional plant biology : FPB.

[88]  M. Fitzgerald,et al.  Application of metabolomics for providing a new generation of selection tools for crop improvement , 2013 .

[89]  D. Huhman,et al.  Mass Spectrometry Strategies in Metabolomics* , 2011, The Journal of Biological Chemistry.

[90]  H. Mock,et al.  Salt stress-induced alterations in the root proteome of barley genotypes with contrasting response towards salinity , 2009, Journal of experimental botany.

[91]  O. Kruse,et al.  Functional analysis of three type-2 DGAT homologue genes for triacylglycerol production in the green microalga Chlamydomonas reinhardtii. , 2012, Journal of biotechnology.

[92]  Floriane L’Haridon,et al.  The cuticle and plant defense to pathogens , 2014, Front. Plant Sci..

[93]  A. Klassen,et al.  Metabolomic Strategies Involving Mass Spectrometry Combined with Liquid and Gas Chromatography. , 2017, Advances in experimental medicine and biology.

[94]  Jürgen Breitenbach,et al.  Transgenic multivitamin corn through biofortification of endosperm with three vitamins representing three distinct metabolic pathways , 2009, Proceedings of the National Academy of Sciences.

[95]  P. Karlovsky,et al.  Relationship between metabolic and genomic diversity in sesame (Sesamum indicum L.) , 2008, BMC Genomics.

[96]  D. C. Uprety,et al.  Rising atmospheric carbon dioxide on grain quality in crop plants , 2010, Physiology and Molecular Biology of Plants.

[97]  E. Ashworth,et al.  Chemically Induced Cuticle Mutation Affecting Epidermal Conductance to Water Vapor and Disease Susceptibility in Sorghum bicolor (L.) Moench , 1994, Plant physiology.

[98]  G. Balogh,et al.  Regulation of desaturase gene expression, changes in membrane lipid composition and freezing tolerance in potato plants , 2007, Molecular Breeding.

[99]  J. Gregory,et al.  Folate biofortification in tomatoes by engineering the pteridine branch of folate synthesis. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[100]  J. Flore,et al.  Influence of Crop Load on Photosynthesis and Dry Matter Partitioning of Seyval Grapevines I. Single Leaf and Whole Vine Response Pre- and Post-harvest , 1993, American Journal of Enology and Viticulture.

[101]  G. Boer,et al.  Terrestrial ecosystems response to future changes in climate and atmospheric CO 2 concentration , 2014 .

[102]  C. Rice-Evans,et al.  The genotypic variation of the antioxidant potential of different tomato varieties , 2005, Free radical research.

[103]  M. Koornneef,et al.  Genetic analysis of seed-soluble oligosaccharides in relation to seed storability of Arabidopsis. , 2000, Plant physiology.

[104]  A. Aharoni,et al.  The strawberry FaMYB1 transcription factor suppresses anthocyanin and flavonol accumulation in transgenic tobacco. , 2001, The Plant journal : for cell and molecular biology.

[105]  G. Forlani,et al.  Metabolism of γ-aminobutyric acid during cold acclimation and freezing and its relationship to frost tolerance in barley and wheat , 2006 .

[106]  J. B. Reid,et al.  Reassessing the Role of N-Hydroxytryptamine in Auxin Biosynthesis1[W][OA] , 2010, Plant Physiology.

[107]  P. Prasad,et al.  Wheat leaf lipids during heat stress: II. Lipids experiencing coordinated metabolism are detected by analysis of lipid co-occurrence. , 2016, Plant, cell & environment.

[108]  T. Altmann,et al.  Phenotypic and metabolic responses to drought and salinity of four contrasting lentil accessions , 2015, Journal of experimental botany.

[109]  M. Horiike,et al.  Isolation and Identification of the Probing Stimulants in the Rice Plant for the White-back Planthopper, Sogatella furcifera (Homoptera: Delphacidae) , 2000, Bioscience, biotechnology, and biochemistry.

[110]  Rui Hai Liu,et al.  Apple phytochemicals and their health benefits , 2004, Nutrition journal.

[111]  Joachim Selbig,et al.  Integration of Metabolomic and Proteomic Phenotypes , 2008, Molecular & Cellular Proteomics.

[112]  Prashanth Suravajhala,et al.  Multi-omic data integration and analysis using systems genomics approaches: methods and applications in animal production, health and welfare , 2016, Genetics Selection Evolution.

[113]  M. Hirai,et al.  Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor. , 2005, The Plant journal : for cell and molecular biology.

[114]  M. Whitecross,et al.  Isovitexin‐2″‐O‐β‐[6‐O‐E‐p‐coumaroylglucopyranoside] from UV‐B irradiated Leaves of Rice, Oryza sativa L. Inhibits Fertility of Helicoverpa armigera , 2007, Photochemistry and photobiology.

[115]  Hezi Tenenboim,et al.  Omic Relief for the Biotically Stressed: Metabolomics of Plant Biotic Interactions. , 2016, Trends in plant science.

[116]  P. Langridge,et al.  Making the most of 'omics' for crop breeding. , 2011, Trends in biotechnology.

[117]  Bjarne Gram Hansen,et al.  Biochemical Networks and Epistasis Shape the Arabidopsis thaliana Metabolome[W] , 2008, The Plant Cell Online.

[118]  A. Fernie,et al.  Co-expression and co-responses: within and beyond transcription , 2012, Front. Plant Sci..

[119]  A. Fernie,et al.  Metabolic variation between japonica and indica rice cultivars as revealed by non-targeted metabolomics , 2014, Scientific Reports.

[120]  Camila Caldana,et al.  Mass spectrometry-based plant metabolomics: Metabolite responses to abiotic stress. , 2016, Mass spectrometry reviews.

[121]  R. Rawat,et al.  Overexpression of Brassica juncea wild-type and mutant HMG-CoA synthase 1 in Arabidopsis up-regulates genes in sterol biosynthesis and enhances sterol production and stress tolerance. , 2012, Plant biotechnology journal.

[122]  W. Kaelin,et al.  Influence of Metabolism on Epigenetics and Disease , 2013, Cell.

[123]  L. Willmitzer,et al.  Using lipidomics for expanding the knowledge on lipid metabolism in plants. , 2016, Biochimie.

[124]  R. Trengove,et al.  Metabolomic profiling and genomic analysis of wheat aneuploid lines to identify genes controlling biochemical pathways in mature grain. , 2016, Plant biotechnology journal.

[125]  E. Blumwald,et al.  Regulated expression of an isopentenyltransferase gene (IPT) in peanut significantly improves drought tolerance and increases yield under field conditions. , 2011, Plant & cell physiology.

[126]  A. Fernie,et al.  Journal of Experimental Botany, Page 1 of 11 Metabolomics and Metabolic Profiling Special Issue , 2004 .

[127]  D. Bioquímica,et al.  MYB10 plays a major role in the regulation of flavonoid/ phenylpropanoid metabolism during ripening of Fragaria × ananassa fruits , 2014 .

[128]  B. Khakimov,et al.  Comprehensive and Comparative Metabolomic Profiling of Wheat, Barley, Oat and Rye Using Gas Chromatography-Mass Spectrometry and Advanced Chemometrics , 2014, Foods.

[129]  Kazuki Saito,et al.  KNApSAcK family databases: integrated metabolite-plant species databases for multifaceted plant research. , 2012, Plant & cell physiology.

[130]  Naama Menda,et al.  Abscisic acid deficiency in the tomato mutant high-pigment 3 leading to increased plastid number and higher fruit lycopene content. , 2008, The Plant journal : for cell and molecular biology.

[131]  M. Bindi,et al.  Free Air CO2 Enrichment of potato (Solanum tuberosum L.): development, growth and yield , 1998 .

[132]  B. Humbel,et al.  Connecting the Molecular Structure of Cutin to Ultrastructure and Physical Properties of the Cuticle in Petals of Arabidopsis1[OPEN] , 2016, Plant Physiology.

[133]  Bin Liao,et al.  Unsaturation of Very-Long-Chain Ceramides Protects Plant from Hypoxia-Induced Damages by Modulating Ethylene Signaling in Arabidopsis , 2015, PLoS genetics.

[134]  S. Nole-Wilson,et al.  Synergistic disruptions in seuss cyp85A2 double mutants reveal a role for brassinolide synthesis during gynoecium and ovule development , 2010, BMC Plant Biology.

[135]  G. Hammer,et al.  Does maintaining green leaf area in sorghum improve yield under drought? II. Dry matter production and yield. , 2000 .

[136]  Cai-guo Xu,et al.  Genetic analysis of the metabolome exemplified using a rice population , 2013, Proceedings of the National Academy of Sciences.

[137]  W. Jin,et al.  IRREGULAR POLLEN EXINE1 Is a Novel Factor in Anther Cuticle and Pollen Exine Formation1[OPEN] , 2016, Plant Physiology.

[138]  J. Franzaring,et al.  Effects of free-air CO2 enrichment on energy traits and seed quality of oilseed rape , 2010 .

[139]  Srivastava,et al.  Delayed ripening of banana fruit by salicylic acid. , 2000, Plant science : an international journal of experimental plant biology.

[140]  M. Szwacka,et al.  Aroma evaluation of transgenic, thaumatin II-producing cucumber fruits. , 2009, Journal of food science.

[141]  J. Šamaj,et al.  Integrating cell biology and proteomic approaches in plants. , 2017, Journal of proteomics.

[142]  Shoshi Kikuchi,et al.  Integrated transcriptomics, proteomics, and metabolomics analyses to survey ozone responses in the leaves of rice seedling. , 2008, Journal of proteome research.

[143]  A. Fernie,et al.  Metabolic analysis of kiwifruit (Actinidia deliciosa) berries from extreme genotypes reveals hallmarks for fruit starch metabolism , 2013, Journal of experimental botany.

[144]  U. Roessner,et al.  Salt-stress induced alterations in the root lipidome of two barley genotypes with contrasting responses to salinity. , 2016, Functional plant biology : FPB.

[145]  A. Yephremov,et al.  Surface lipids and plant defenses. , 2009, Plant physiology and biochemistry : PPB.

[146]  E. Hinchliffe,et al.  Improving the nutritional value of Golden Rice through increased pro-vitamin A content , 2005, Nature Biotechnology.

[147]  L. Willmitzer,et al.  Analysis of short-term changes in the Arabidopsis thaliana glycerolipidome in response to temperature and light. , 2011, The Plant journal : for cell and molecular biology.

[148]  R. E. Sharp,et al.  Abscisic acid accumulation maintains maize primary root elongation at low water potentials by restricting ethylene production. , 2000, Plant physiology.

[149]  V. Chandler,et al.  Paramutation: epigenetic instructions passed across generations. , 2008, Genetics.

[150]  Kazuki Saito,et al.  Metabolic Profiling of Developing Pear Fruits Reveals Dynamic Variation in Primary and Secondary Metabolites, Including Plant Hormones , 2015, PloS one.

[151]  N. Springer,et al.  Brd1 Gene in Maize Encodes a Brassinosteroid C-6 Oxidase , 2012, PloS one.

[152]  Jean-Jack M. Riethoven,et al.  Arabidopsis MSH1 mutation alters the epigenome and produces heritable changes in plant growth , 2015, Nature Communications.

[153]  C. Chapple,et al.  Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana , 2015, Proceedings of the National Academy of Sciences.

[154]  D. Bartels,et al.  Lipid signalling in plant responses to abiotic stress. , 2016, Plant, cell & environment.

[155]  R. Hellens,et al.  An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae , 2010, BMC Plant Biology.

[156]  S. Komatsu,et al.  Comprehensive analysis of mitochondria in roots and hypocotyls of soybean under flooding stress using proteomics and metabolomics techniques. , 2011, Journal of proteome research.

[157]  Rameshwar Sharma,et al.  Natural variation in folate levels among tomato (Solanum lycopersicum) accessions. , 2017, Food chemistry.

[158]  L. Goulao,et al.  A focus on the biosynthesis and composition of cuticle in fruits. , 2015, Journal of agricultural and food chemistry.

[159]  R. Ramautar,et al.  Recent developments in liquid-phase separation techniques for metabolomics. , 2014, Bioanalysis.

[160]  R. Goodacre,et al.  Biochemical Analyses of Sorghum Varieties Reveal Differential Responses to Drought , 2016, PloS one.

[161]  Jenny Renaut,et al.  The quest for tolerant varieties: the importance of integrating “omics” techniques to phenotyping , 2015, Front. Plant Sci..

[162]  S. Rudaz,et al.  Metabolomics reveals herbivore-induced metabolites of resistance and susceptibility in maize leaves and roots. , 2013, Plant, cell & environment.

[163]  L. Xiong,et al.  Identification of defense-related rice genes by suppression subtractive hybridization and differential screening. , 2001, Molecular plant-microbe interactions : MPMI.

[164]  Martin J. Mueller,et al.  Lipid Profiling of the Arabidopsis Hypersensitive Response Reveals Specific Lipid Peroxidation and Fragmentation Processes: Biogenesis of Pimelic and Azelaic Acid1[C][W] , 2012, Plant Physiology.

[165]  M. Mikulič-Petkovšek,et al.  Importance of metabolite distribution in apple fruit , 2017 .

[166]  T. Veenstra,et al.  Analytical and statistical approaches to metabolomics research. , 2009, Journal of separation science.

[167]  Marc‐André D'Aoust,et al.  Antisense Inhibition of Tomato Fruit Sucrose Synthase Decreases Fruit Setting and the Sucrose Unloading Capacity of Young Fruit , 1999, Plant Cell.

[168]  M. Udvardi,et al.  Comparative ionomics and metabolomics in extremophile and glycophytic Lotus species under salt stress challenge the metabolic pre-adaptation hypothesis. , 2011, Plant, cell & environment.

[169]  Masanori Arita,et al.  MS-DIAL: Data Independent MS/MS Deconvolution for Comprehensive Metabolome Analysis , 2015, Nature Methods.

[170]  Ep Heuvelink,et al.  Quantifying the source–sink balance and carbohydrate content in three tomato cultivars , 2015, Front. Plant Sci..

[171]  J. Franzaring,et al.  Effects of CO2 Enrichment and Drought on Photosynthesis, Growth and Yield of an Old and a Modern Barley Cultivar , 2016 .

[172]  Graham J King,et al.  A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening , 2006, Nature Genetics.

[173]  G. Hwang,et al.  Characterization of wines from grape varieties through multivariate statistical analysis of 1H NMR spectroscopic data , 2009 .

[174]  M. Matsuoka,et al.  Identifying and exploiting grain yield genes in rice. , 2008, Current opinion in plant biology.

[175]  C. Honda,et al.  Isolation and functional analysis of a MYB transcription factor gene that is a key regulator for the development of red coloration in apple skin. , 2007, Plant & cell physiology.

[176]  G. Farquhar,et al.  Overproduction of Abscisic Acid in Tomato Increases Transpiration Efficiency and Root Hydraulic Conductivity and Influences Leaf Expansion1[OA] , 2007, Plant Physiology.

[177]  Christian Gieger,et al.  Epigenetics meets metabolomics: an epigenome-wide association study with blood serum metabolic traits , 2013, Human molecular genetics.

[178]  Takayuki Tohge,et al.  Identification of Conserved and Diverse Metabolic Shifts during Rice Grain Development , 2016, Scientific Reports.

[179]  Bernd Markus Lange,et al.  Open-Access Metabolomics Databases for Natural Product Research: Present Capabilities and Future Potential , 2015, Front. Bioeng. Biotechnol..

[180]  C. Patrick,et al.  Role of Serotonin and Dopamine System Interactions in the Neurobiology of Impulsive Aggression and its Comorbidity with other Clinical Disorders. , 2008, Aggression and violent behavior.

[181]  Takayuki Tohge,et al.  Web-based resources for mass-spectrometry-based metabolomics: a user's guide. , 2009, Phytochemistry.

[182]  A. Barabasi,et al.  Interactome Networks and Human Disease , 2011, Cell.

[183]  R. Jones,et al.  Improvement of tomato flavor by genetically increasing sugar and acid contents , 1983, Euphytica.

[184]  R. Jetter,et al.  Sealing plant surfaces: cuticular wax formation by epidermal cells. , 2008, Annual review of plant biology.

[185]  O. Fiehn,et al.  Metabolomic Assessment of Key Maize Resources: GC-MS and NMR Profiling of Grain from B73 Hybrids of the Nested Association Mapping (NAM) Founders and of Geographically Diverse Landraces. , 2016, Journal of agricultural and food chemistry.

[186]  R. Hall,et al.  Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors , 2008, Nature Biotechnology.

[187]  Rod Jones,et al.  Class targeted metabolomics: ESI ion trap screening methods for glucosinolates based on MSn fragmentation. , 2008, Phytochemistry.

[188]  G. Kruppa,et al.  Metabolomics applications of FT-ICR mass spectrometry. , 2005, Mass spectrometry reviews.

[189]  P. Kachroo,et al.  Fatty Acid-derived signals in plant defense. , 2009, Annual review of phytopathology.

[190]  Joost T. van Dongen,et al.  Analysis of alanine aminotransferase in various organs of soybean (Glycine max) and in dependence of different nitrogen fertilisers during hypoxic stress , 2010, Amino Acids.

[191]  W. Wagoner,et al.  Reduced ethylene synthesis by transgenic tomatoes expressing S-adenosylmethionine hydrolase , 1994, Plant Molecular Biology.

[192]  Corinne Le Quéré,et al.  Climate Change 2013: The Physical Science Basis , 2013 .

[193]  J. Metraux,et al.  The cuticle as source of signals for plant defense , 2005 .

[194]  S. Idso,et al.  Effects of atmospheric CO(2) enrichment on plant constituents related to animal and human health. , 2001, Environmental and experimental botany.

[195]  Floriane L’Haridon,et al.  A Permeable Cuticle Is Associated with the Release of Reactive Oxygen Species and Induction of Innate Immunity , 2011, PLoS pathogens.

[196]  A. Fernie,et al.  Metabolomics-assisted breeding: a viable option for crop improvement? , 2009, Trends in genetics : TIG.

[197]  F. Davies,et al.  Hypobaria and hypoxia affects growth and phytochemical contents of lettuce. , 2009 .

[198]  M. Hawkesford,et al.  Temperature determines size and direction of effects of elevated CO2 and nitrogen form on yield quantity and quality of Chinese cabbage. , 2016, Plant biology.

[199]  Kazuki Saito,et al.  Integrated metabolomics and phytochemical genomics approaches for studies on rice , 2016, GigaScience.

[200]  A. Fernie,et al.  Genetic Determinants of the Network of Primary Metabolism and Their Relationships to Plant Performance in a Maize Recombinant Inbred Line Population[OPEN] , 2015, Plant Cell.

[201]  P. Panigrahi,et al.  Fusarium oxysporum mediates systems metabolic reprogramming of chickpea roots as revealed by a combination of proteomics and metabolomics , 2016, Plant biotechnology journal.

[202]  Ze Yun,et al.  Comparative proteomic and metabolomic profiling of citrus fruit with enhancement of disease resistance by postharvest heat treatment , 2013, BMC Plant Biology.

[203]  Joost T. van Dongen,et al.  Glycolysis and the Tricarboxylic Acid Cycle Are Linked by Alanine Aminotransferase during Hypoxia Induced by Waterlogging of Lotus japonicus1[W][OA] , 2010, Plant Physiology.

[204]  F. Aragão,et al.  Folate biofortification of lettuce by expression of a codon optimized chicken GTP cyclohydrolase I gene , 2009, Transgenic Research.

[205]  S. Zhong,et al.  Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening , 2013, Nature Biotechnology.

[206]  Rajeev K. Varshney,et al.  Proteomics and Metabolomics: Two Emerging Areas for Legume Improvement , 2015, Front. Plant Sci..

[207]  J. Sodré,et al.  Potential vegetable sources for biodiesel production: cashew, coconut and cotton , 2015, Materials for Renewable and Sustainable Energy.

[208]  M. Sussman,et al.  Metabolomic profiling reveals suppression of oxylipin biosynthesis during the early stages of legume–rhizobia symbiosis , 2012, FEBS letters.

[209]  Adrian Bird,et al.  Perceptions of epigenetics , 2007, Nature.

[210]  S. Setha Roles of Abscisic Acid in Fruit Ripening , 2012 .

[211]  H. Heyman,et al.  The potential of mass spectrometry imaging in plant metabolomics: a review , 2015, Phytochemistry Reviews.

[212]  Jiri Adamec,et al.  Development of GCxGC/TOF-MS metabolomics for use in ecotoxicological studies with invertebrates. , 2008, Aquatic toxicology.

[213]  J. Shah Lipids, lipases, and lipid-modifying enzymes in plant disease resistance. , 2005, Annual review of phytopathology.

[214]  Yi-Zeng Liang,et al.  Feature extraction from resolution perspective for gas chromatography-mass spectrometry datasets , 2016 .

[215]  D. Taub,et al.  Why are nitrogen concentrations in plant tissues lower under elevated CO2? A critical examination of the hypotheses. , 2008, Journal of integrative plant biology.

[216]  Sonia J. Miller,et al.  Metabolomic and elemental profiling of melon fruit quality as affected by genotype and environment , 2013, Metabolomics.

[217]  L. Willmitzer,et al.  GC–MS metabolic profiling of Cabernet Sauvignon and Merlot cultivars during grapevine berry development and network analysis reveals a stage- and cultivar-dependent connectivity of primary metabolites , 2016, Metabolomics.

[218]  T. Lodha,et al.  Proteomics: A Successful Approach to Understand the Molecular Mechanism of Plant-Pathogen Interaction , 2013 .

[219]  A. Hamilton,et al.  Altered fruit ripening and leaf senescence in tomatoes expressing an antisense ethylene‐forming enzyme transgene , 1993 .

[220]  Kazuki Saito,et al.  Role of Metabolomics in Crop Improvement , 2012, Journal of Plant Biochemistry and Biotechnology.

[221]  Kazuo Shinozaki,et al.  Arabidopsis Cys2/His2-Type Zinc-Finger Proteins Function as Transcription Repressors under Drought, Cold, and High-Salinity Stress Conditions1 , 2004, Plant Physiology.

[222]  C. Benning,et al.  DGD1-independent biosynthesis of extraplastidic galactolipids after phosphate deprivation in Arabidopsis. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[223]  F. Carrari,et al.  Enhanced Photosynthetic Performance and Growth as a Consequence of Decreasing Mitochondrial Malate Dehydrogenase Activity in Transgenic Tomato Plants1 , 2005, Plant Physiology.

[224]  A. Albacete,et al.  Hormonal and metabolic regulation of source-sink relations under salinity and drought: from plant survival to crop yield stability. , 2014, Biotechnology advances.

[225]  Heinz-Werner Klein,et al.  Liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR MS): an early overview , 2004, Analytical and bioanalytical chemistry.

[226]  Kazuki Saito,et al.  Application of a metabolomic method combining one-dimensional and two-dimensional gas chromatography-time-of-flight/mass spectrometry to metabolic phenotyping of natural variants in rice. , 2007, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[227]  Kazuki Saito,et al.  Identification of a Flavonol 7-O-Rhamnosyltransferase Gene Determining Flavonoid Pattern in Arabidopsis by Transcriptome Coexpression Analysis and Reverse Genetics*♦ , 2007, Journal of Biological Chemistry.

[228]  P. Beyer,et al.  Engineering the provitamin A (beta-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm. , 2000, Science.

[229]  Uday K. Divi,et al.  Brassinosteroid: a biotechnological target for enhancing crop yield and stress tolerance. , 2009, New biotechnology.

[230]  F. Tardieu,et al.  Drought and Abscisic Acid Effects on Aquaporin Content Translate into Changes in Hydraulic Conductivity and Leaf Growth Rate: A Trans-Scale Approach1[W][OA] , 2009, Plant Physiology.

[231]  S. C. O T,et al.  Potential Effects of Warming and Drying on Peatland Plant Community Composition , 2022 .

[232]  Christian Kappel,et al.  Recent advances in the transcriptional regulation of the flavonoid biosynthetic pathway. , 2011, Journal of experimental botany.

[233]  M. Burger,et al.  Nitrate assimilation is inhibited by elevated CO 2 in field-grown wheat , 2014 .

[234]  Xiuxin Deng,et al.  GABA Pathway Rate-Limit Citrate Degradation in Postharvest Citrus Fruit Evidence from HB Pumelo (Citrus grandis) × Fairchild (Citrus reticulata) Hybrid Population. , 2017, Journal of agricultural and food chemistry.

[235]  Litao Yang,et al.  Plant Metabolomics: An Indispensable System Biology Tool for Plant Science , 2016, International journal of molecular sciences.

[236]  Yaping Zhao,et al.  Enrichment of β-carotene from palm oil using supercritical carbon dioxide pretreatment-solvent extraction technique , 2017 .

[237]  B. Misra,et al.  Updates in metabolomics tools and resources: 2014–2015 , 2016, Electrophoresis.

[238]  C. Junot,et al.  Investigating the plant response to cadmium exposure by proteomic and metabolomic approaches , 2011, Proteomics.

[239]  R. Hellens,et al.  Red colouration in apple fruit is due to the activity of the MYB transcription factor, MdMYB10 , 2007, The Plant journal : for cell and molecular biology.

[240]  X. Zhang,et al.  Lipid profiling and tolerance to low-temperature stress in Thellungiella salsuginea in comparison with Arabidopsis thaliana , 2013, Biologia Plantarum.

[241]  A. Aharoni,et al.  The transcription factor SlSHINE3 modulates defense responses in tomato plants , 2013, Plant Molecular Biology.

[242]  D. Roby,et al.  Very long chain fatty acid and lipid signaling in the response of plants to pathogens , 2009, Plant signaling & behavior.

[243]  S. Idso,et al.  Effects of atmospheric CO(2) enrichment on plant constituents related to animal and human health. , 2001, Environmental and experimental botany.

[244]  M. Elhiti,et al.  Abnormal development and altered hormone profile and sensitivity in Arabidopsis plants ectopically expressing Brassica shoot apical meristem genes , 2012 .

[245]  P. G. Dominguez,et al.  Natural occurring epialleles determine vitamin E accumulation in tomato fruits , 2014, Nature Communications.

[246]  R. Storey,et al.  Engineering the anthocyanin regulatory complex of strawberry (Fragaria vesca) , 2014, Front. Plant Sci..

[247]  T. Dunn,et al.  An Inositolphosphorylceramide Synthase Is Involved in Regulation of Plant Programmed Cell Death Associated with Defense in Arabidopsis[C][W] , 2008, The Plant Cell Online.

[248]  Kazuki Saito,et al.  Using metabolomic approaches to explore chemical diversity in rice. , 2014, Molecular plant.

[249]  J. Zou,et al.  Adjustments of lipid pathways in plant adaptation to temperature stress , 2016, Plant signaling & behavior.

[250]  S. Storozhenko,et al.  Folate fortification of rice by metabolic engineering , 2007, Nature Biotechnology.

[251]  B. Malathi,et al.  Agrobacterium-mediated genetic transformation and production of semilooper resistant transgenic castor (Ricinus communis L.) , 2006, Euphytica.

[252]  M. Hertog,et al.  Targeted metabolomics study of ‘Braeburn’ apples during long-term storage , 2014 .

[253]  H. Mol,et al.  metAlignID: a high-throughput software tool set for automated detection of trace level contaminants in comprehensive LECO two-dimensional gas chromatography time-of-flight mass spectrometry data. , 2012, Journal of chromatography. A.

[254]  Zhentian Lei,et al.  MET-XAlign: a metabolite cross-alignment tool for LC/MS-based comparative metabolomics. , 2015, Analytical chemistry.

[255]  A. Sharma,et al.  Role of plant hormones and their interplay in development and ripening of fleshy fruits. , 2013, Journal of experimental botany.

[256]  J. Pereira,et al.  Understanding plant responses to drought - from genes to the whole plant. , 2003, Functional plant biology : FPB.

[257]  C. Skibola,et al.  Influences of diet and the gut microbiome on epigenetic modulation in cancer and other diseases , 2015, Clinical Epigenetics.

[258]  A. Allan,et al.  Coordinated regulation of anthocyanin biosynthesis in Chinese bayberry (Myrica rubra) fruit by a R2R3 MYB transcription factor , 2010, Planta.

[259]  K. Feldmann,et al.  Brassinosteroids Regulate Grain Filling in Rice[W][OA] , 2008, The Plant Cell Online.

[260]  A. Fernie,et al.  Combining Quantitative Genetics Approaches with Regulatory Network Analysis to Dissect the Complex Metabolism of the Maize Kernel1[OPEN] , 2015, Plant Physiology.

[261]  W. Vriezen,et al.  The Solanum lycopersicum auxin response factor 7 (SlARF7) regulates auxin signaling during tomato fruit set and development. , 2009, The Plant journal : for cell and molecular biology.

[262]  P. Oeller,et al.  Reversible inhibition of tomato fruit senescence by antisense RNA. , 1991, Science.

[263]  Nigel W. Hardy,et al.  Plant Metabolomics , 2002, The Plant Cell Online.

[264]  A. Bloom,et al.  CO2 enrichment inhibits shoot nitrate assimilation in C3 but not C4 plants and slows growth under nitrate in C3 plants. , 2012, Ecology.

[265]  Luguang Wu,et al.  Doubled sugar content in sugarcane plants modified to produce a sucrose isomer. , 2007, Plant biotechnology journal.

[266]  S. Zhong,et al.  Tomato GOLDEN2-LIKE Transcription Factors Reveal Molecular Gradients That Function during Fruit Development and Ripening[W][OPEN] , 2014, Plant Cell.

[267]  A. Saydut,et al.  Process optimization for production of biodiesel from hazelnut oil, sunflower oil and their hybrid feedstock , 2016 .

[268]  R. Bino,et al.  Intra- and inter-metabolite correlation spectroscopy of tomato metabolomics data obtained by liquid chromatography-mass spectrometry and nuclear magnetic resonance , 2008, Metabolomics.

[269]  N. Singh,et al.  Whole genome sequences in pulse crops: a global community resource to expedite translational genomics and knowledge-based crop improvement , 2015, Biotechnology Letters.

[270]  Xiaofeng Cao,et al.  Epigenetic Mutation of RAV6 Affects Leaf Angle and Seed Size in Rice1[OPEN] , 2015, Plant Physiology.

[271]  Takayuki Tohge,et al.  From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics , 2017, GigaScience.

[272]  Pilar Cubas,et al.  An epigenetic mutation responsible for natural variation in ̄ oral symmetry , 2022 .

[273]  Kazuki Saito,et al.  Rice Metabolomics , 2008, Rice.

[274]  G. Fitzgerald,et al.  Elevated atmospheric [CO2] can dramatically increase wheat yields in semi‐arid environments and buffer against heat waves , 2016, Global change biology.

[275]  M. Nam,et al.  Network analysis of the metabolome and transcriptome reveals novel regulation of potato pigmentation , 2016, Journal of experimental botany.

[276]  H. Gautier,et al.  Number of cells in tomato fruit depending on fruit position and source-sink balance during plant development , 2002, Plant Growth Regulation.

[277]  C. Reuzeau,et al.  Boosting Crop Yields with Plant Steroids[W] , 2012, Plant Cell.

[278]  C. Broeckling,et al.  Non-targeted Metabolomics in Diverse Sorghum Breeding Lines Indicates Primary and Secondary Metabolite Profiles Are Associated with Plant Biomass Accumulation and Photosynthesis , 2016, Front. Plant Sci..

[279]  P. Trivedi,et al.  Changes in activities of cell wall hydrolases during ethylene-induced ripening in banana: effect of 1-MCP, ABA, and IAA , 2004 .

[280]  W. Vriezen,et al.  The Solanum lycopersicum AUXIN RESPONSE FACTOR 7 (SlARF7) mediates cross-talk between auxin and gibberellin signalling during tomato fruit set and development , 2010, Journal of experimental botany.

[281]  Akira Oikawa,et al.  Exploring molecular backgrounds of quality traits in rice by predictive models based on high-coverage metabolomics , 2011, BMC Systems Biology.

[282]  E. Grotewold,et al.  MYB transcription factors in Arabidopsis. , 2002, Trends in plant science.

[283]  Wolfram Weckwerth,et al.  Integration of metabolomics and proteomics in molecular plant physiology--coping with the complexity by data-dimensionality reduction. , 2008, Physiologia Plantarum : An International Journal for Plant Biology.

[284]  Cristina E Davis,et al.  The Highs and Lows of FAIMS: Predictions and Future Trends for High Field Asymmetric Waveform Ion Mobility Spectrometry. , 2012, Journal of nanomedicine & nanotechnology.

[285]  I. Levin,et al.  ANTHOCYANIN1 from Solanum chilense is more efficient in accumulating anthocyanin metabolites than its Solanumlycopersicum counterpart in association with the ANTHOCYANIN FRUIT phenotype of tomato , 2012, Theoretical and Applied Genetics.

[286]  Shuhui Song,et al.  Comparative metabolomic analysis reveals a reactive oxygen species-dominated dynamic model underlying chilling environment adaptation and tolerance in rice. , 2016, The New phytologist.

[287]  E. Pichersky,et al.  Enhanced levels of the aroma and flavor compound S-linalool by metabolic engineering of the terpenoid pathway in tomato fruits. , 2001, Plant physiology.

[288]  J. W. Peters,et al.  Engineering algae for biohydrogen and biofuel production. , 2009, Current opinion in biotechnology.

[289]  G. Barry,et al.  Control of ethylene synthesis by expression of a bacterial enzyme in transgenic tomato plants. , 1991, The Plant cell.

[290]  P. Beyer,et al.  Transcriptional-Metabolic Networks in β-Carotene-Enriched Potato Tubers: The Long and Winding Road to the Golden Phenotype1[C][W][OA] , 2010, Plant Physiology.

[291]  L. Jaakola,et al.  New insights into the regulation of anthocyanin biosynthesis in fruits. , 2013, Trends in plant science.

[292]  Amritpal S. Singh,et al.  Biotechnological approaches for the genetic improvement of Jatropha curcas L.: A biodiesel plant , 2015 .

[293]  D. Grierson,et al.  Antisense gene that inhibits synthesis of the hormone ethylene in transgenic plants , 1990, Nature.

[294]  J. Snape,et al.  Location of a gene for frost resistance on chromosome 5A of wheat , 1989, Euphytica.

[295]  C. Rothan,et al.  The expression of cell proliferation-related genes in early developing flowers is affected by a fruit load reduction in tomato plants , 2006 .

[296]  M. Scheffer,et al.  Increase of atmospheric CO2 promotes phytoplankton productivity , 2004 .

[297]  Ricardo Natalino,et al.  Wild Brazilian Mustard (Brassica juncea L.) Seed Oil Methyl Esters as Biodiesel Fuel , 2009 .

[298]  J. Gershenzon,et al.  Comparative quantitative trait loci mapping of aliphatic, indolic and benzylic glucosinolate production in Arabidopsis thaliana leaves and seeds. , 2001, Genetics.

[299]  Faye M. Rosin,et al.  Transcriptome and Metabolite Profiling Show That APETALA2a Is a Major Regulator of Tomato Fruit Ripening[C][W] , 2011, Plant Cell.

[300]  Siddharth Jain,et al.  Pongamia as a Source of Biodiesel in India , 2011 .

[301]  P. Arruda Genetically modified sugarcane for bioenergy generation. , 2012, Current opinion in biotechnology.

[302]  Lothar Willmitzer,et al.  Linking Gene Expression and Membrane Lipid Composition of Arabidopsis[W][OPEN] , 2014, Plant Cell.

[303]  Malcolm J Hawkesford,et al.  An integrated approach to crop genetic improvement. , 2012, Journal of integrative plant biology.

[304]  Jian Ye,et al.  Development of marker-free transgenic Jatropha plants with increased levels of seed oleic acid , 2012, Biotechnology for Biofuels.

[305]  B. Asselbergh,et al.  Abscisic Acid Deficiency Causes Changes in Cuticle Permeability and Pectin Composition That Influence Tomato Resistance to Botrytis cinerea1[C][W][OA] , 2010, Plant Physiology.

[306]  Xiuxin Deng,et al.  A novel bud mutation that confers abnormal patterns of lycopene accumulation in sweet orange fruit (Citrus sinensis L. Osbeck). , 2007, Journal of experimental botany.

[307]  Alexander Goesmann,et al.  ALLocator: An Interactive Web Platform for the Analysis of Metabolomic LC-ESI-MS Datasets, Enabling Semi-Automated, User-Revised Compound Annotation and Mass Isotopomer Ratio Analysis , 2014, PloS one.

[308]  S. Takumi,et al.  A major quantitative trait locus for cold-responsive gene expression is linked to frost-resistance gene Fr-A2 in common wheat , 2013, Breeding science.

[309]  P. Fraser,et al.  Metabolite profiling of carotenoid and phenolic pathways in mutant and transgenic lines of tomato: identification of a high antioxidant fruit line. , 2006, Phytochemistry.

[310]  J. Flore,et al.  Influence of Crop Load on Photosynthesis and Dry Matter Partitioning of Seyval Grapevines. III. Seasonal Changes in Dry Matter Partitioning, Vine Morphology, Yield, and Fruit Composition , 1995, American Journal of Enology and Viticulture.

[311]  P. Fraser,et al.  A genome-wide metabolomic resource for tomato fruit from Solanum pennellii , 2012, Scientific Reports.

[312]  Wei Chen,et al.  Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism , 2014, Nature Genetics.

[313]  A. R. Walker,et al.  Light-Induced Expression of a MYB Gene Regulates Anthocyanin Biosynthesis in Red Apples1 , 2006, Plant Physiology.

[314]  A. Fernie,et al.  Silencing of the Mitochondrial Ascorbate Synthesizing Enzyme l-Galactono-1,4-Lactone Dehydrogenase Affects Plant and Fruit Development in Tomato1[W][OA] , 2007, Plant Physiology.

[315]  V. Ortiz-Martínez,et al.  In-depth study of the transesterification reaction of Pongamia pinnata oil for biodiesel production using catalyst-free supercritical methanol process , 2016 .

[316]  Chiara Tonelli,et al.  How Can Research on Plants Contribute to Promoting Human Health?[OA] , 2011, Plant Cell.

[317]  G. Hammer,et al.  Does maintaining green leaf area in sorghum improve yield under drought? I. Leaf growth and senescence , 2000 .

[318]  P. Raymond,et al.  High hexokinase activity in tomato fruit perturbs carbon and energy metabolism and reduces fruit and seed size , 2004 .

[319]  J. Mach Identification of a Novel Maize Protein Important for Paramutation at the purple plant1 Locus , 2012, Plant Cell.

[320]  Jonathan D. G. Jones,et al.  Anthocyanins Double the Shelf Life of Tomatoes by Delaying Overripening and Reducing Susceptibility to Gray Mold , 2013, Current Biology.

[321]  J. Coleman,et al.  Elevated CO2 increases productivity and invasive species success in an arid ecosystem , 2000, Nature.

[322]  M. Muthamilarasan,et al.  Exploration of millet models for developing nutrient rich graminaceous crops. , 2016, Plant science : an international journal of experimental plant biology.

[323]  C. Vance,et al.  Legumes: Importance and Constraints to Greater Use , 2003, Plant Physiology.

[324]  U. Roessner,et al.  Root spatial metabolite profiling of two genotypes of barley (Hordeum vulgare L.) reveals differences in response to short-term salt stress , 2016, Journal of experimental botany.

[325]  G. Glauser,et al.  Lipid Antioxidant and Galactolipid Remodeling under Temperature Stress in Tomato Plants , 2016, Front. Plant Sci..

[326]  Kazuo Shinozaki,et al.  Landscape of the lipidome and transcriptome under heat stress in Arabidopsis thaliana , 2015, Scientific Reports.

[327]  G. Khush Green revolution: the way forward , 2001, Nature Reviews Genetics.

[328]  Karsten Niehaus,et al.  Effects of atmospheric CO2 enrichment on biomass, yield and low molecular weight metabolites in wheat grain , 2010 .

[329]  J. Metraux,et al.  A permeable cuticle in Arabidopsis leads to a strong resistance to Botrytis cinerea , 2007, The EMBO journal.

[330]  A. Fernie,et al.  Metabolic Profiling of a Mapping Population Exposes New Insights in the Regulation of Seed Metabolism and Seed, Fruit, and Plant Relations , 2012, PLoS genetics.

[331]  Nuno Carvalhais,et al.  Enhanced seasonal CO2 exchange caused by amplified plant productivity in northern ecosystems , 2016, Science.

[332]  Rising atmospheric CO2 may affect oil quality and seed yield of sunflower (Helianthus annus L.) , 2014, Acta Physiologiae Plantarum.

[333]  Bart Nicolai,et al.  Effect of browning related pre- and postharvest factors on the ‘Braeburn’ apple metabolome during CA storage , 2016 .

[334]  A. Rathore,et al.  Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects , 2016, Front. Plant Sci..

[335]  C. Chevalier,et al.  Fruit growth-related genes in tomato. , 2015, Journal of experimental botany.

[336]  S. Baud,et al.  Regulation of HSD1 in seeds of Arabidopsis thaliana. , 2009, Plant & cell physiology.

[337]  Concepción Sánchez-Moreno,et al.  An exploratory NMR nutri-metabonomic investigation reveals dimethyl sulfone as a dietary biomarker for onion intake. , 2009, The Analyst.

[338]  D. Choi,et al.  Metabolomic Characterization of Hot Pepper (Capsicum annuum "CM334") during Fruit Development. , 2015, Journal of agricultural and food chemistry.

[339]  Kazuki Saito,et al.  Dissection of genotype-phenotype associations in rice grains using metabolome quantitative trait loci analysis. , 2012, The Plant journal : for cell and molecular biology.

[340]  J. Flintham,et al.  Genetic Control of Storage Oil Synthesis in Seeds of Arabidopsis1 , 2004, Plant Physiology.

[341]  R. Nelson,et al.  Smaller than predicted increase in aboveground net primary production and yield of field‐grown soybean under fully open‐air [CO2] elevation , 2005 .

[342]  J. Araus,et al.  Metabolite Profiles of Maize Leaves in Drought, Heat, and Combined Stress Field Trials Reveal the Relationship between Metabolism and Grain Yield1[OPEN] , 2015, Plant Physiology.

[343]  G. Blanc,et al.  Lipidomic and transcriptomic analyses of Chlamydomonas reinhardtii under heat stress unveil a direct route for the conversion of membrane lipids into storage lipids. , 2016, Plant, cell & environment.

[344]  L. Marcelis,et al.  Sink strength as a determinant of dry matter partitioning in the whole plant. , 1996, Journal of experimental botany.

[345]  Tianzhen Zhang,et al.  Epigenomic and functional analyses reveal roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons , 2017, Genome Biology.

[346]  M. Bange,et al.  Plant-soil interactions and nutrient availability determine the impact of elevated CO2 and temperature on cotton productivity , 2016, Plant and Soil.

[347]  A. Fernie,et al.  Metabolomics-Inspired Insight into Developmental, Environmental and Genetic Aspects of Tomato Fruit Chemical Composition and Quality. , 2015, Plant & cell physiology.

[348]  W. J. Davies,et al.  ABA-based chemical signalling: the co-ordination of responses to stress in plants. , 2002, Plant, cell & environment.

[349]  Hideyuki Suzuki,et al.  Development of transgenic plants in jatropha with drought tolerance , 2012 .

[350]  Lieven Sterck,et al.  Genetical metabolomics of flavonoid biosynthesis in Populus: a case study. , 2006, The Plant journal : for cell and molecular biology.

[351]  M. Sujatha,et al.  Role of biotechnological interventions in the improvement of castor (Ricinus communis L.) and Jatropha curcas L. , 2008, Biotechnology advances.

[352]  K. Cone,et al.  Paramutation: The Chromatin Connection , 2004, The Plant Cell Online.

[353]  D. Hincha,et al.  Identification of Drought Tolerance Markers in a Diverse Population of Rice Cultivars by Expression and Metabolite Profiling , 2013, PloS one.

[354]  Jianbing Yan,et al.  Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights , 2014, Nature Communications.

[355]  S. Wienkoop,et al.  Microbial symbionts affect Pisum sativum proteome and metabolome under Didymella pinodes infection. , 2016, Journal of proteomics.

[356]  Oliver Yu,et al.  Metabolic profiling of strawberry (Fragaria x ananassa Duch.) during fruit development and maturation. , 2011, Journal of experimental botany.

[357]  M. Thomas,et al.  White grapes arose through the mutation of two similar and adjacent regulatory genes. , 2007, The Plant journal : for cell and molecular biology.

[358]  Henrik Antti,et al.  Multi-platform mass spectrometry analysis of the CSF and plasma metabolomes of rigorously matched amyotrophic lateral sclerosis, Parkinson's disease and control subjects. , 2016, Molecular bioSystems.

[359]  G. Cuzzuol,et al.  Growth, photosynthate partitioning and fructan accumulation in plants of Vernonia herbacea (Vell.) Rusby under two nitrogen levels , 2005 .

[360]  F. Stampar,et al.  Alteration of the content of primary and secondary metabolites in strawberry fruit by Colletotrichum nymphaeae infection. , 2013, Journal of agricultural and food chemistry.

[361]  M. Sarwar,et al.  The importance of cereals (Poaceae: Gramineae) nutrition in human health: A review , 2013 .

[362]  M. Guidarelli,et al.  Polyphenols Variation in Fruits of the Susceptible Strawberry Cultivar Alba during Ripening and upon Fungal Pathogen Interaction and Possible Involvement in Unripe Fruit Tolerance. , 2016, Journal of agricultural and food chemistry.

[363]  Xin Zhang,et al.  Overexpression of Folate Biosynthesis Genes in Rice (Oryza sativa L.) and Evaluation of Their Impact on Seed Folate Content , 2014, Plant Foods for Human Nutrition.

[364]  Alencar Xavier,et al.  Genetic Architecture of Phenomic-Enabled Canopy Coverage in Glycine max , 2017, Genetics.