SE161:/DS2

Sample Set Information

ID	TSE1320
Title	Dissection of genotype-phenotype associations in rice grains using metabolome quantitative trait loci analysis.
Description	A comprehensive and large-scale metabolome quantitative trait loci (mQTL) analysis was performed to investigate the genetic backgrounds associated with metabolic phenotypes in rice grains. The metabolome dataset consisted of 759 metabolite signals obtained from the grains of 85 lines of rice (Oryza sativa, Sasanishiki x Habataki back-crossed inbred lines). Metabolome analysis was performed using four mass spectrometry pipelines to enhance detection of different classes of metabolites. This mQTL analysis of a wide range of metabolites highlighted an uneven distribution of 802 mQTLs on the rice genome, as well as different modes of metabolic trait (m-trait) control among various types of metabolites. The levels of most metabolites within rice grains were highly sensitive to environmental factors, but only weakly associated with mQTLs. Coordinated control was observed for several groups of metabolites, such as amino acids linked to the mQTL hotspot on chromosome 3. For flavonoids, m-trait variation among the experimental lines was tightly governed by genetic factors that alter the glycosylation of flavones. Many loci affecting levels of metabolites were detected by QTL analysis, and plausible gene candidates were evaluated by in silico analysis. Several mQTLs profoundly influenced metabolite levels, providing insight into the control of rice metabolism. The genomic region and genes potentially responsible for the biosynthesis of apigenin-6,8-di-C-α-l-arabinoside are presented as an example of a critical mQTL identified by the analysis.
Authors	Matsuda F, Okazaki Y, Oikawa A, Kusano M, Nakabayashi R, Kikuchi J, Yonemaru J, Ebana K, Yano M, Saito K.
Reference	Plant J. 2012 May;70(4):624-36. doi: 10.1111/j.1365-313X.2012.04903.x. Epub 2012 Feb 10.
Comment

PubMed

Data Analysis Details Information

ID	DS2
Title	Data processing and analisys (GC-TOF-MS)
Description	The experimental procedures for the GC-, CE- and LC-IT-TOF-MS pipelines were as reported previously (Kusano et al., 2007b; Okazaki et al., 2009; Oikawa et al., 2011). For GC-TOF-MS analysis, metabolite levels were determined by a single analysis due to technical issues. For GC- and CE-TOF-MS data, a total of 84 and 38 rice seed metabolites, respectively, were identified by comparing the chromatographic behaviour of the metabolites with that of standard compounds.
Comment_of_details	Kusano et al., J Chromatogr B Analyt Technol Biomed Life Sci. 2007 Aug;855(1):71-9. Epub 2007 May 16.

PubMed