SE161:/DS1
From Metabolonote
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 |
Data Analysis Details Information
| ID | DS1 |
|---|---|
| Title | Data processing and analisys (LC-ESI-Q-TOF-MS) |
| Description | Metabolome analysis and data processing were performed as described previously (Matsuda et al., 2009, 2010). Briefly, the metabolome data were obtained in the positive ion mode (m/z 100–2000; dwell time 0.45 sec; inter-scan delay 0.05 sec), from which a data matrix was generated using MetAlign (De Vos et al., 2007; Lommen, 2009). The metabolite signals commonly detected from both the 2005 and 2007 harvest datasets were used for subsequent analysis, and a data matrix containing mean values for 362 metabolite intensities from 510 runs (85 experimental lines x two yearly harvests x three analytical replicates) was produced. |
| Comment_of_details |
