| MS Description
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Analysis was performed using samples with … Analysis was performed using samples with three or four biological replicates per cultivar. Frozen rice tissue was homogenized in five volumes of cold 80% aqueous methanol containing an internal standard (0.5 mgL-1 lidocaine, Tokyo Kasei, Tokyo, Japan, http://www.tcichemicals.com/), using a mixer mill (MM 300, Retsch, Haan, Germany, http://www.retsch.com/) and a zirconia bead for 6 min at 20 Hz. Samples were centrifuged at 15 000 g for 10 min.
The supernatant (3 μl) were subsequently subjected to metabolome analysis using liquid chromatography coupled with electrospray quadrupole time-of-flight tandem mass spectrometry with an Acquity BEH ODS column (LC-ESI-QToF/MS, HPLC: Waters Acquity UPLC system; MS: Waters QToF Premier, http://www.waters.com/). Metabolome analysis and data processing were conducted according to a previously described method (Matsuda et al., 2009, 2010). Briefly, metabolome data were obtained in positive ion mode (m/z 100–2000; dwell time: 0.5 sec), from which a data matrix was generated by MetAlign2 (Lommen and Kools, 2012). Signal intensities were normalized by dividing them by the intensities of the internal standard (lidocaine). A data matrix containing the 342 metabolite intensities from 668 runs was produced for the Japanese rice population (Tables S2 and S3). panese rice population (Tables S2 and S3).
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