SE161:/S1/M3/D1
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 |
Sample Information
| ID | S1 |
|---|---|
| Title | Rice |
| Organism - Scientific Name | Oryza sativa |
| Organism - ID | NCBI taxonomy:4530 |
| Compound - ID | |
| Compound - Source | |
| Preparation | The plant population consisted of 85 back‐crossed inbred lines derived from the cross Sasanishiki/Habataki//Sasanishiki///Sasanishiki (Sasanishiki x Habataki) (Nagata et al., 2002b). Seeds from the experimental lines were grown in a paddy field at the National Institute of Agrobiological Sciences (Tsukuba, Japan) in 2005 and 2007, employing similar cultivation schedules. The seeds of the 2005 and 2007 harvests were used for metabolome analysis. One hundred dehulled seeds obtained from whole seeds harvested from 10 independent plants were ground to a fine powder using an MM300 mixer mill (Retsch, http://www.retsch.com/) at 20Hz for 2min in a stainless steel grinding vessel. The powder was divided between small sample tubes (50–100mg) under nitrogen, and the samples were stored at −80°C until analysis. |
| Sample Preparation Details ID | |
| Comment |
Analytical Method Information
| ID | M3 |
|---|---|
| Title | LC-IT-TOF-MS |
| Method Details ID | MS3 |
| Sample Amount | |
| Comment |
Analytical Method Details Information
| ID | MS3 |
|---|---|
| Title | LC-IT-TOF-MS |
| Instrument | LC, Shimadzu LC-20AD system; MS, Shimadzu LCMS-IT-TOF |
| Instrument Type | |
| Ionization | ESI |
| Ion Mode | positive and negative |
| Description | Sample metabolomic data were acquired using four time-of-flight mass spectrometers (TOF-MS), including CE-TOF-MS for analysis of polar metabolites, GC-TOF-MS for analysis of primary metabolites, LC-Q-TOF-MS for analysis of secondary metabolites and LC-IT-TOF-MS for analysis of lipids. Analysis was performed in triplicate, and the samples were extracted from each pipeline using optimized methods.
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| Comment_of_details | Okazaki et al., Plant Cell. 2009 Mar;21(3):892-909. doi: 10.1105/tpc.108.063925. Epub 2009 Mar 13. |
Data Analysis Information
| ID | D1 |
|---|---|
| Title | Data Processing and Analysis (LC-IT-TOF-MS) |
| Data Analysis Details ID | DS3 |
| Recommended decimal places of m/z | |
| Comment |
Data Analysis Details Information
| ID | DS3 |
|---|---|
| Title | Data processing and analisys (LC-IT-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). In addition to three γ-oryzanols, three lysophosphatidylcholine and 17 triacylglycerol compounds were identified as mixtures of several structural isomers by lipid analysis using LC-IT-TOF-MS. When an identical metabolite was detected using different analytical methods, the data with a higher signal-to-noise ratio were used for subsequent analysis. |
| Comment_of_details | Okazaki et al., Plant Cell. 2009 Mar;21(3):892-909. doi: 10.1105/tpc.108.063925. Epub 2009 Mar 13. |
