Integrated metabolomics and phytochemical genomics approaches for studies on rice

Integrated metabolomics for abiotic stress responses in plants

(2015) Ryo Nakabayashi et al.   CURRENT OPINION IN PLANT BIOLOGY

High night temperature strongly impacts TCA cycle, amino acid and polyamine biosynthetic pathways in rice in a sensitivity-dependent manner

(2015) Ulrike Glaubitz et al.   JOURNAL OF EXPERIMENTAL BOTANY

Using Metabolomic Approaches to Explore Chemical Diversity in Rice

(2015) Miyako Kusano et al.   Molecular Plant

Spatiotemporal Distribution of Phenolamides and the Genetics of Natural Variation of Hydroxycinnamoyl Spermidine in Rice

(2015) Xuekui Dong et al.   Molecular Plant

The Tyrosine Aminomutase TAM1 Is Required for β-Tyrosine Biosynthesis in Rice

(2015) Jian Yan et al.   PLANT CELL

Metabolic and transcriptomic signatures of rice floral organs reveal sugar starvation as a factor in reproductive failure under heat and drought stress

(2015) Xia Li et al.   PLANT CELL AND ENVIRONMENT

Integrated Metabolomics and Transcriptomics Reveal Enhanced Specialized Metabolism inMedicago truncatulaRoot Border Cells

(2015) Bonnie S. Watson et al.   PLANT PHYSIOLOGY

OsATG7 is required for autophagy-dependent lipid metabolism in rice postmeiotic anther development

(2014) Takamitsu Kurusu et al.   Autophagy

Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism

(2014) Wei Chen et al.   NATURE GENETICS

Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism

(2014) Fumio Matsuda et al.   PLANT JOURNAL

Precision genome editing in plants via gene targeting andpiggyBac-mediated marker excision

(2014) Ayako Nishizawa-Yokoi et al.   PLANT JOURNAL

Integrated Analysis of the Effects of Cold and Dehydration on Rice Metabolites, Phytohormones, and Gene Transcripts

(2014) K. Maruyama et al.   PLANT PHYSIOLOGY

Metabolic variation between japonica and indica rice cultivars as revealed by non-targeted metabolomics

(2014) Chaoyang Hu et al.   Scientific Reports

The 3,000 rice genomes project

(2014)   GigaScience

Phytochemical genomics — a new trend

(2013) Kazuki Saito   CURRENT OPINION IN PLANT BIOLOGY

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) Zhigang Yang et al.   Metabolomics

A Novel Integrated Method for Large-Scale Detection, Identification, and Quantification of Widely Targeted Metabolites: Application in the Study of Rice Metabolomics

(2013) Wei Chen et al.   Molecular Plant

Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice

(2013) Wenzhi Jiang et al.   NUCLEIC ACIDS RESEARCH

Identification of Drought Tolerance Markers in a Diverse Population of Rice Cultivars by Expression and Metabolite Profiling

(2013) Thomas Degenkolbe et al.   PLoS One

Genetic analysis of the metabolome exemplified using a rice population

(2013) L. Gong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploring molecular backgrounds of quality traits in rice by predictive models based on high-coverage metabolomics

(2012) Henning Redestig et al.   BMC Systems Biology

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

Plant secondary metabolite profiling evidences strain-dependent effect in the Azospirillum–Oryza sativa association

(2012) Amel Chamam et al.   PHYTOCHEMISTRY

Suppression of α-amylase genes improves quality of rice grain ripened under high temperature

(2012) Makoto Hakata et al.   PLANT BIOTECHNOLOGY JOURNAL

Dissection of genotype-phenotype associations in rice grains using metabolome quantitative trait loci analysis

(2012) Fumio Matsuda et al.   PLANT JOURNAL

Making sense of low oxygen sensing

(2012) Julia Bailey-Serres et al.   TRENDS IN PLANT SCIENCE

Genome-wide Transcriptional Profiling of Appressorium Development by the Rice Blast Fungus Magnaporthe oryzae

(2012) Darren M. Soanes et al.   PLoS Pathogens

Differential Metabolic Regulation Governed by the Rice SUB1A Gene during Submergence Stress and Identification of Alanylglycine by 1H NMR Spectroscopy

(2011) Gregory A. Barding et al.   JOURNAL OF PROTEOME RESEARCH

A genomics and multi-platform metabolomics approach to identify new traits of rice quality in traditional and improved varieties

(2011) M. N. Calingacion et al.   Metabolomics

Deciphering Starch Quality of Rice Kernels Using Metabolite Profiling and Pedigree Network Analysis

(2011) Miyako Kusano et al.   Molecular Plant

The Biotron Breeding System: A Rapid and Reliable Procedure for Genetic Studies and Breeding in Rice

(2011) Takayuki Ohnishi et al.   PLANT AND CELL PHYSIOLOGY

Metabolomics data reveal a crucial role of cytosolic glutamine synthetase 1;1 in coordinating metabolic balance in rice

(2011) Miyako Kusano et al.   PLANT JOURNAL

Application of Gene Targeting to Designed Mutation Breeding of High-Tryptophan Rice

(2011) H. Saika et al.   PLANT PHYSIOLOGY

Genetic, proteomic and metabolic analysis of the regulation of energy storage in rice seedlings in response to drought

(2011) Liebo Shu et al.   PROTEOMICS

Metabolomic and transcriptomic analysis of the rice response to the bacterial blight pathogen Xanthomonas oryzae pv. oryzae

(2010) Theodore R. Sana et al.   Metabolomics

Atlas of Rice Grain Filling-Related Metabolism under High Temperature: Joint Analysis of Metabolome and Transcriptome Demonstrated Inhibition of Starch Accumulation and Induction of Amino Acid Accumulation

(2010) Hiromoto Yamakawa et al.   PLANT AND CELL PHYSIOLOGY

Metabolome and Photochemical Analysis of Rice Plants Overexpressing Arabidopsis NAD Kinase Gene

(2010) K. Takahara et al.   PLANT PHYSIOLOGY

Metabolomic and Functional Genomic Analyses Reveal Varietal Differences in Bioactive Compounds of Cooked Rice

(2010) Adam L. Heuberger et al.   PLoS One

Q-TARO: QTL Annotation Rice Online Database

(2010) Jun-ichi Yonemaru et al.   Rice

Rice-Arabidopsis FOX line screening with FT-NIR-based fingerprinting for GC-TOF/MS-based metabolite profiling

(2009) Makoto Suzuki et al.   Metabolomics

Metabolomic Screening Applied to Rice FOX Arabidopsis Lines Leads to the Identification of a Gene-Changing Nitrogen Metabolism

(2009) Doris Albinsky et al.   Molecular Plant

Metabolome Analysis of Response to Oxidative Stress in Rice Suspension Cells Overexpressing Cell Death Suppressor Bax Inhibitor-1

(2009) Toshiki Ishikawa et al.   PLANT AND CELL PHYSIOLOGY

Advancing Genetic Theory and Application by Metabolic Quantitative Trait Loci Analysis

(2009) DanielJ. Kliebenstein   PLANT CELL

Metabolomic analysis reveals a common pattern of metabolic re-programming during invasion of three host plant species byMagnaporthe grisea

(2009) David Parker et al.   PLANT JOURNAL

Not just a grain of rice: the quest for quality

(2009) Melissa A. Fitzgerald et al.   TRENDS IN PLANT SCIENCE

Time-resolved metabolomics reveals metabolic modulation in rice foliage

(2008) Shigeru Sato et al.   BMC Systems Biology

Integrated Transcriptomics, Proteomics, and Metabolomics Analyses To Survey Ozone Responses in the Leaves of Rice Seedling

(2008) Kyoungwon Cho et al.   JOURNAL OF PROTEOME RESEARCH

Widely Targeted Metabolomics Based on Large-Scale MS/MS Data for Elucidating Metabolite Accumulation Patterns in Plants

(2008) Yuji Sawada et al.   PLANT AND CELL PHYSIOLOGY

The tryptophan pathway is involved in the defense responses of rice against pathogenic infection via serotonin production

(2008) Atsushi Ishihara et al.   PLANT JOURNAL

Metabolomics-assisted breeding: a viable option for crop improvement?

(2008) Alisdair R. Fernie et al.   TRENDS IN GENETICS

Rice Metabolomics

(2008) Akira Oikawa et al.   Rice