Using metabolomic approaches to explore chemical diversity in rice.

[1]  Andrew R. Jakubowski,et al.  Assessing metabolomic and chemical diversity of a soybean lineage representing 35 years of breeding , 2015, Metabolomics.

[2]  Atsushi Fukushima,et al.  A network perspective on nitrogen metabolism from model to crop plants using integrated 'omics' approaches. , 2014, Journal of experimental botany.

[3]  Kazuki Saito,et al.  Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism , 2014, The Plant journal : for cell and molecular biology.

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

[5]  Jun Wang,et al.  The 3,000 rice genomes project: new opportunities and challenges for future rice research , 2014, GigaScience.

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

[7]  T. Huan,et al.  IsoMS: automated processing of LC-MS data generated by a chemical isotope labeling metabolomics platform. , 2014, Analytical chemistry.

[8]  J. Kopka,et al.  Annotating unknown components from GC/EI-MS-based metabolite profiling experiments using GC/APCI(+)-QTOFMS , 2014, Metabolomics.

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

[10]  Yvan Saeys,et al.  Systematic Structural Characterization of Metabolites in Arabidopsis via Candidate Substrate-Product Pair Networks[C][W] , 2014, Plant Cell.

[11]  Hideyuki Suzuki,et al.  Integrated Analysis of the Effects of Cold and Dehydration on Rice Metabolites, Phytohormones, and Gene Transcripts1[W][OPEN] , 2014, Plant Physiology.

[12]  Mark H. Wright,et al.  Natural variation of rice strigolactone biosynthesis is associated with the deletion of two MAX1 orthologs , 2014, Proceedings of the National Academy of Sciences.

[13]  M. Fitzgerald,et al.  Diversity of Global Rice Markets and the Science Required for Consumer-Targeted Rice Breeding , 2014, PloS one.

[14]  Tetsuya Mori,et al.  Toward better annotation in plant metabolomics: isolation and structure elucidation of 36 specialized metabolites from Oryza sativa (rice) by using MS/MS and NMR analyses , 2013, Metabolomics.

[15]  Kazuki Saito,et al.  Toward better annotation in plant metabolomics: isolation and structure elucidation of 36 specialized metabolites from Oryza sativa (rice) by using MS/MS and NMR analyses , 2013, Metabolomics.

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

[17]  C. Delatorre,et al.  Stress-Induced Cytokinin Synthesis Increases Drought Tolerance through the Coordinated Regulation of Carbon and Nitrogen Assimilation in Rice1[C][W][OPEN] , 2013, Plant Physiology.

[18]  Zhikang Li,et al.  Temporal profiling of primary metabolites under chilling stress and its association with seedling chilling tolerance of rice (Oryza sativa L.) , 2013, Rice.

[19]  Oliver Fiehn,et al.  LipidBlast - in-silico tandem mass spectrometry database for lipid identification , 2013, Nature Methods.

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

[21]  Bifeng Yuan,et al.  A selective pretreatment method for determination of endogenous active brassinosteroids in plant tissues: double layered solid phase extraction combined with boronate affinity polymer monolith microextraction , 2013, Plant Methods.

[22]  J. Sheen,et al.  Glucose–TOR signalling reprograms the transcriptome and activates meristems , 2013, Nature.

[23]  Kazuki Saito,et al.  Metabolomics for unknown plant metabolites , 2013, Analytical and Bioanalytical Chemistry.

[24]  M. Hirai,et al.  A new class of plant lipid is essential for protection against phosphorus depletion , 2013, Nature Communications.

[25]  M. Schmid,et al.  Regulation of Flowering by Trehalose-6-Phosphate Signaling in Arabidopsis thaliana , 2013, Science.

[26]  R. Peters,et al.  The Role of Momilactones in Rice Allelopathy , 2013, Journal of Chemical Ecology.

[27]  M. Hirai,et al.  Combination of liquid chromatography-Fourier transform ion cyclotron resonance-mass spectrometry with 13C-labeling for chemical assignment of sulfur-containing metabolites in onion bulbs. , 2013, Analytical chemistry.

[28]  K. Akiyama,et al.  Confirming Stereochemical Structures of Strigolactones Produced by Rice and Tobacco , 2012, Molecular plant.

[29]  S. Wongpornchai,et al.  Quantification of flavonoids in black rice by liquid chromatography-negative electrospray ionization tandem mass spectrometry. , 2012, Journal of agricultural and food chemistry.

[30]  Yutaka Yamada,et al.  RIKEN tandem mass spectral database (ReSpect) for phytochemicals: a plant-specific MS/MS-based data resource and database. , 2012, Phytochemistry.

[31]  K. H. Laursen,et al.  A genomics and multi-platform metabolomics approach to identify new traits of rice quality in traditional and improved varieties , 2012, Metabolomics.

[32]  Ralf Tautenhahn,et al.  An accelerated workflow for untargeted metabolomics using the METLIN database , 2012, Nature Biotechnology.

[33]  Xu-dong Zhu,et al.  The rice hydroperoxide lyase OsHPL3 functions in defense responses by modulating the oxylipin pathway. , 2012, The Plant journal : for cell and molecular biology.

[34]  Kazunori Okada,et al.  The potential bioproduction of the pharmaceutical agent sakuranetin, a flavonoid phytoalexin in rice , 2012, Bioengineered.

[35]  Min Shi,et al.  Identification of quantitative trait Loci for lipid metabolism in rice seeds. , 2012, Molecular plant.

[36]  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.

[37]  Andrew D Hanson,et al.  Frontiers in metabolic reconstruction and modeling of plant genomes. , 2012, Journal of experimental botany.

[38]  Kazuki Saito,et al.  Deciphering starch quality of rice kernels using metabolite profiling and pedigree network analysis. , 2012, Molecular plant.

[39]  Jie Chen,et al.  Determination of flavor components of rice bran by GC-MS and chemometrics , 2012 .

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

[41]  C. Bachem,et al.  Untargeted Metabolic Quantitative Trait Loci Analyses Reveal a Relationship between Primary Metabolism and Potato Tuber Quality1[W][OA] , 2012, Plant Physiology.

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

[43]  Magali Schnell Ramos,et al.  Toward the Storage Metabolome: Profiling the Barley Vacuole1[W][OA] , 2011, Plant Physiology.

[44]  Yozo Okazaki,et al.  Recent advances of metabolomics in plant biotechnology , 2011, Plant Biotechnology Reports.

[45]  Kazuki Saito,et al.  Exploring matrix effects and quantification performance in metabolomics experiments using artificial biological gradients. , 2011, Analytical chemistry.

[46]  Y. Choi,et al.  NMR-based plant metabolomics: where do we stand, where do we go? , 2011, Trends in biotechnology.

[47]  A. Fukushima,et al.  Metabolomics data reveal a crucial role of cytosolic glutamine synthetase 1;1 in coordinating metabolic balance in rice. , 2011, The Plant journal : for cell and molecular biology.

[48]  Kazuki Saito,et al.  Covering Chemical Diversity of Genetically-Modified Tomatoes Using Metabolomics for Objective Substantial Equivalence Assessment , 2011, PloS one.

[49]  Kazuki Saito,et al.  Metabolomic approaches toward understanding nitrogen metabolism in plants. , 2011, Journal of experimental botany.

[50]  J. K. Kim,et al.  Variation and correlation analysis of flavonoids and carotenoids in Korean pigmented rice (Oryza sativa L.) cultivars. , 2010, Journal of agricultural and food chemistry.

[51]  Jian-Min Zhou,et al.  Tricin—a potential multifunctional nutraceutical , 2010, Phytochemistry Reviews.

[52]  M. Hirai,et al.  MassBank: a public repository for sharing mass spectral data for life sciences. , 2010, Journal of mass spectrometry : JMS.

[53]  Shinjiro Yamaguchi,et al.  Contribution of Strigolactones to the Inhibition of Tiller Bud Outgrowth under Phosphate Deficiency in Rice , 2010, Plant & cell physiology.

[54]  Matthias Müller-Hannemann,et al.  In silico fragmentation for computer assisted identification of metabolite mass spectra , 2010, BMC Bioinformatics.

[55]  Kazuki Saito,et al.  Phosphoenolpyruvate carboxylase intrinsically located in the chloroplast of rice plays a crucial role in ammonium assimilation , 2010, Proceedings of the National Academy of Sciences.

[56]  S. Yanagisawa,et al.  Metabolome and Photochemical Analysis of Rice Plants Overexpressing Arabidopsis NAD Kinase Gene1[W][OA] , 2010, Plant Physiology.

[57]  G. Ren,et al.  Antioxidant and alpha-glucosidase inhibitory activity of colored grains in China. , 2010, Journal of agricultural and food chemistry.

[58]  N. Tuteja,et al.  Polyamines and abiotic stress tolerance in plants , 2010, Plant signaling & behavior.

[59]  O. Fiehn,et al.  FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. , 2009, Analytical chemistry.

[60]  Xian-Jun Song,et al.  The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water , 2009, Nature.

[61]  C. Brondani,et al.  Microsatellite marker-mediated analysis of the EMBRAPA Rice Core Collection genetic diversity , 2009, Genetica.

[62]  M. Matsuoka,et al.  Highly sensitive and high-throughput analysis of plant hormones using MS-probe modification and liquid chromatography-tandem mass spectrometry: an application for hormone profiling in Oryza sativa. , 2009, Plant & cell physiology.

[63]  M. Fitzgerald,et al.  Not just a grain of rice: the quest for quality. , 2009, Trends in plant science.

[64]  A. Mitchell,et al.  Influence of cooking on anthocyanins in black rice (Oryza sativa L. japonica var. SBR). , 2009, Journal of agricultural and food chemistry.

[65]  J. Delcour,et al.  Carotenoids in raw and parboiled brown and milled rice. , 2008, Journal of agricultural and food chemistry.

[66]  David S. Wishart,et al.  HMDB: a knowledgebase for the human metabolome , 2008, Nucleic Acids Res..

[67]  Y. Kamiya,et al.  Inhibition of shoot branching by new terpenoid plant hormones , 2008, Nature.

[68]  Jingyuan Fu,et al.  Integrative analyses of genetic variation in enzyme activities of primary carbohydrate metabolism reveal distinct modes of regulation in Arabidopsis thaliana , 2008, Genome Biology.

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

[70]  J. Selbig,et al.  Mode of Inheritance of Primary Metabolic Traits in Tomato[W][OA] , 2008, The Plant Cell Online.

[71]  John L Markley,et al.  Metabolite identification via the Madison Metabolomics Consortium Database , 2008, Nature Biotechnology.

[72]  O. Fiehn,et al.  Identification of metabolic and biomass QTL in Arabidopsis thaliana in a parallel analysis of RIL and IL populations , 2007, The Plant journal : for cell and molecular biology.

[73]  Z. T. Nehus,et al.  Quantification of Vitamin E and γ-Oryzanol Components in Rice Germ and Bran , 2007 .

[74]  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.

[75]  Fabrice Davrieux,et al.  Rapid discrimination of scented rice by solid-phase microextraction, mass spectrometry, and multivariate analysis used as a mass sensor. , 2007, Journal of agricultural and food chemistry.

[76]  S. Seo,et al.  Contribution of Ethylene Biosynthesis for Resistance to Blast Fungus Infection in Young Rice Plants1[OA] , 2006, Plant Physiology.

[77]  K. Akiyama,et al.  Strigolactones: chemical signals for fungal symbionts and parasitic weeds in plant roots. , 2006, Annals of botany.

[78]  J. Young,et al.  Anthocyanin composition in black, blue, pink, purple, and red cereal grains. , 2006, Journal of agricultural and food chemistry.

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

[80]  Wei Zhao,et al.  Gramene: a bird's eye view of cereal genomes , 2005, Nucleic Acids Res..

[81]  M. Kawase,et al.  Development of an RFLP-based Rice Diversity Research Set of Germplasm , 2005 .

[82]  V. Ghole,et al.  Molecular characterization of marker-free transgenic lines of indica rice that accumulate carotenoids in seed endosperm , 2005, Molecular Genetics and Genomics.

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

[84]  H. Ohta,et al.  Three Enzyme Systems for Galactoglycerolipid Biosynthesis Are Coordinately Regulated in Plants* , 2005, Journal of Biological Chemistry.

[85]  Christoph Steinbeck,et al.  NMRShiftDB -- compound identification and structure elucidation support through a free community-built web database. , 2004, Phytochemistry.

[86]  Masaru Tomita,et al.  Simultaneous determination of the main metabolites in rice leaves using capillary electrophoresis mass spectrometry and capillary electrophoresis diode array detection. , 2004, The Plant journal : for cell and molecular biology.

[87]  Kozo Nakamura,et al.  Analysis of phenolic compounds in white rice, brown rice, and germinated brown rice. , 2004, Journal of agricultural and food chemistry.

[88]  J. Hyun,et al.  Cyanidin and Malvidin from Oryza sativa cv. Heugjinjubyeo mediate cytotoxicity against human monocytic leukemia cells by arrest of G(2)/M phase and induction of apoptosis. , 2004, Journal of agricultural and food chemistry.

[89]  J. G. Wu,et al.  Methods of developing core collections based on the predicted genotypic value of rice (Oryza sativa L.) , 2004, Theoretical and Applied Genetics.

[90]  Y. Hayata,et al.  Variation of 2-Acetyl-1-Pyrroline Concentration in Aromatic Rice Grains Collected in the Same Region in Japan and Factors Affecting Its Concentration , 2004 .

[91]  T. Badger,et al.  Characterization of triterpene alcohol and sterol ferulates in rice bran using LC-MS/MS. , 2003, Journal of agricultural and food chemistry.

[92]  Richard A Dixon,et al.  Phytochemistry meets genome analysis, and beyond. , 2003, Phytochemistry.

[93]  C. Vance,et al.  Phosphorus acquisition and use: critical adaptations by plants for securing a nonrenewable resource. , 2003, The New phytologist.

[94]  P. Schieberle,et al.  Comparison of key aroma compounds in cooked brown rice varieties based on aroma extract dilution analyses. , 2002, Journal of agricultural and food chemistry.

[95]  H. Chung,et al.  A quinolone alkaloid with antioxidant activity from the aleurone layer of anthocyanin-pigmented rice. , 2001, Journal of natural products.

[96]  Zhimin Xu,et al.  Antioxidant activity of tocopherols, tocotrienols, and gamma-oryzanol components from rice bran against cholesterol oxidation accelerated by 2,2'-azobis(2-methylpropionamidine) dihydrochloride. , 2001, Journal of agricultural and food chemistry.

[97]  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.

[98]  M. Matsuoka,et al.  Loss of Function of a Rice brassinosteroid insensitive1 Homolog Prevents Internode Elongation and Bending of the Lamina Joint , 2000, Plant Cell.

[99]  T. Akihisa,et al.  Triterpene alcohol and sterol ferulates from rice bran and their anti-inflammatory effects. , 2000, Journal of agricultural and food chemistry.

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

[101]  K. Feldmann,et al.  Brassinosteroid-insensitive dwarf mutants of Arabidopsis accumulate brassinosteroids. , 1999, Plant physiology.

[102]  C. Kao,et al.  Excess copper induces an accumulation of putrescine in rice leaves , 1999 .

[103]  Z. Xu,et al.  Purification and identification of components of gamma-oryzanol in rice bran Oil. , 1999, Journal of agricultural and food chemistry.

[104]  E. M. Faergestad,et al.  Grain Development Mutants of Barley ([alpha]-Amylase Production during Grain Maturation and Its Relation to Endogenous Gibberellic Acid Content) , 1997, Plant physiology.

[105]  M. Wootton,et al.  Changes in Volatile Components of Paddy, Brown and White Fragrant Rice During Storage , 1996 .

[106]  N. Terahara,et al.  Composition of Anthocyanin Pigments in Aromatic Red Rice and its Wine , 1994 .

[107]  H. Kato,et al.  Oryzalexin E, A diterpene phytoalexin from UV-irradiated rice leaves , 1993 .

[108]  O. Kodama,et al.  Novel Phytoalexins (Oryzalexins A, B and C) Isolated from Rice Blast Leaves Infected with Pyricularia oryzae. Part I: Isolation, Characterization and Biological Activities of Oryzalexins , 1985 .

[109]  O. Kodama,et al.  Novel Phytoalexins (Oryzalexins A, B and C) Isolated from Rice Blast Leaves Infected with Pyricularia oryzae. , 1985 .

[110]  J. Maga Rice product volatiles: a review , 1984 .

[111]  E. Grill,et al.  Exploring the Arabidopsis sulfur metabolome. , 2014, The Plant journal : for cell and molecular biology.

[112]  Robert D Hall,et al.  Solid phase micro-extraction GC-MS analysis of natural volatile components in melon and rice. , 2012, Methods in molecular biology.

[113]  E. Berghofer,et al.  Physicochemical and antioxidative properties of red and black rice varieties from Thailand, China and Sri Lanka , 2011 .

[114]  A. Fukushima,et al.  Metabolomic screening applied to rice FOX Arabidopsis lines leads to the identification of a gene-changing nitrogen metabolism. , 2010, Molecular plant.

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

[116]  Jin-Chul Shin,et al.  Characterization of antioxidant alkaloids and phenolic acids from anthocyanin-pigmented rice (Oryza sativa cv. Heugjinjubyeo) , 2007 .

[117]  J. Kopka,et al.  Comparative Metabolome Analysis of the Salt Response in Breeding Cultivars of Rice , 2007 .

[118]  Robert Yawadio,et al.  Identification of phenolic compounds isolated from pigmented rices and their aldose reductase inhibitory activities , 2007 .

[119]  Z. T. Nehus,et al.  Quantification of vitamin E and gamma-oryzanol components in rice germ and bran. , 2007, Journal of agricultural and food chemistry.

[120]  K. L. Heong,et al.  Rice is life: scientific perspectives for the 21st century. Proceedings of the World Rice Research Conference held in Tsukuba, Japan, 4-7 November 2004. , 2005 .

[121]  N. Allan Concepts and controversy , 1997 .

[122]  S. Kiyosawa,et al.  Sakuranetin, a flavanone phytoalexin from ultraviolet-irradiated rice leaves , 1992 .

[123]  R. Buttery 2-Acetyl-1-pyrroline : An important aroma component of cooked rice , 1982 .