IC4R006-Metabolomics-2007-17556050

Project Title

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

The Background of This Projec

• Two-dimensional gas chromatography GC × GC-TOF/MS is a novel approach for enhancing the GC resolution, and it has great advantages in increasing the resolution and peak capacity over the one dimensional separation method. The GC × GC-TOF/MS for metabolomics has been applied for com- plex metabolite profiles from mouse spleen [21]. This is the first report for the use of a technique which significantly enhances metabolite resolution. Currently, the GC × GC-TOF/MS technique has been applied in the analysis of volatile compounds [22,23] and also in the analysis of metabolite mixtures from mouse tissue, yeast cells, and human urine and serum as the comprehensive GC × GC-TOF/MS analysis [24–27].
• When non-targeted metabolic profiling data are subjected to multivariate statistical analysis such as principal component analysis (PCA) and partial least square-discriminate analysis (PLS-DA) toward the obtained data, a high throughput and high accuracy can be achieved for clustering according to the vectors of numerous metabolites.
• In order to develop a technique for studies in plant metabolomics, we have developed a combined method, namely, 1D- and GC × GC-TOF/MS. We applied this technique in the non-targeted metabolic profiling of brown rice seeds from the world rice core collection (WRC). The WRC is a representative set of Asian cultivated rice, Oryza sativa L., comprising 69 vari- eties selected from 3000 accessions stored in the Genebank of the National Institute of Agrobiological Sciences (NIAS), Japan, classified based on DNA polymorphism [28]. The WRC covers ca. 90% of the DNA polymorphisms detected in the original population and can be used as a convenient set to survey the genetic diversity of rice. Therefore, the metabolic phenotyping of the WRC varieties gives us an insight on the representative metabolite diversity of rice natural variants.
• In this project, the researchers describes a metabolomic method combining 1D-GC-TOF/MS and GC × GC-TOF/MS analyses and an example of its application to focus on the differences in the characteristics of data obtained from 1D-GC/MS and GC × GC/MS measurements of the WRC samples. This study presents the first report of the initial metabolic phenotyping in brown rice seeds of the WRC.

Labs working on this Project

• RIKEN Plant Science Center, 1-7-22 Yokohama, Kanagawa 230-0045, Japan
• Group for Chemometrics, Organic Chemistry, Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
• Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 87 Umeå, Sweden
• National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
• Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan

Corresponding Author

Miyako Kusano (E-mail:mkusano005@psc.riken.jp)