## 3 Materials and Methods
### Extraction and Analysis of Hydrophilic Compounds  
Hydrophilic compounds (amino acids, organic acids, sugars, phenolic acids, and sugar alcohols) were extracted as previously described [29]. Briefly, 100 mg of ground rice samples were placed in 2 mL tubes with 1 mL of methanol:chloroform:water (2.5:1:1, _v/v/v_) solution. Then, 60 \(\mu\)L of ribitol (200 \(\mu\)g/mL in methanol) was added as an internal standard (IS). After vortexing, the samples were incubated at 37 \({}^{\circ}\)C for 30 min, with shaking at 1200 rpm. Next, the mixtures were centrifuged at 16,000\(\times\)\(g\) for 3 min at 4 \({}^{\circ}\)C. The supernatant (800 \(\mu\)L) was transferred to a new 2 mL tube and mixed with 400 \(\mu\)L of deionized water. The samples were centrifuged again at 16,000\(\times\)\(g\) for 3 min at 4 \({}^{\circ}\)C, and 900 \(\mu\)L of the supernatant were transferred to a new tube. The solvent was completely evaporated in a centrifugal concentrator (CC-105, TOMY, Tokyo, Japan) for 3 h and freeze-dried at \(-80\)\({}^{\circ}\)C for at least 16 h. For derivatization, the samples were treated with 80 \(\mu\)L of methoxyamine hydrochloride in pyridine (20 mg/mL) and incubated at 30 \({}^{\circ}\)C for 90 min in a thermomixer (model 5355, Eppendorf AG, Hamburg, Germany), with shaking at 1200 rpm. Next, 80 \(\mu\)L of MSTFA was added, and the samples incubated at 37 \({}^{\circ}\)C for 30 min, with shaking at 1200 rpm. The derivatized samples (80 \(\mu\)L) were transferred to glass inserts in GC auto sampler vials. The hydrophilic compounds were analyzed using Agilent 7890A GC (Agilent, Santa Clara, CA, USA) coupled to a Pegasus 4D TOF-MS (LECO, St. Joseph, MI, USA). Helium gas was passed at a rate of 1.20 mL/min. Thereafter, 1 \(\mu\)L of the extracted sample was injected in a 1:25 ratio split mode, and the inlet temperature was set at 250 \({}^{\circ}\)C. Rtx-5 MS (0.25 mm \(\times\) 0.25 \(\mu\)m \(\times\) 30 m; Restek, Bellefonte, PA, USA) and Rvi-17 sil MS (0.15 mm \(\times\) 0.15 \(\mu\)m \(\times\) 1.2 m; Restek, Bellefonte, PA, USA) were used as the first and second column, respectively, for GC\(\times\)GC-TOF-MS. The conditions for each column were set individually. The oven temperature was programmed as follows: the oven temperature for the first column was maintained at 80 \({}^{\circ}\)C for 0.5 min, followed by ramping to 330 \({}^{\circ}\)C at 5 \({}^{\circ}\)C/min, and then holding at this temperature for 5 min. The oven temperature for the second column was set with 5 \({}^{\circ}\)C offset from the first column temperature. The modulator temperature program was 15 \({}^{\circ}\)C offset above the second column temperature. The modulation period was set to 4 s, with 0.6 s hot and 1.4 s cool pulse durations. The ion source and transfer line temperatures were set at 230 \({}^{\circ}\)C and 260 \({}^{\circ}\)C, respectively. The data were acquired over an _m_/z mass range of 45-650, and the detector voltage was set to 1700 V. Qualitative analysis of peaks was performed using the Chroma TOF software (version 4.5, LECO, St. Joseph, MI, USA), and peaks were identified based on the mass spectral data by comparing with in-house libraries, NIST, and Wiley9 (Figure S4 and Table S13). The quantitative estimation was based on peak area ratios relative to the IS peak area (Table S2).