||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).