Metabolomic Profiling of Heat Tolerance During Grain Filling in Rice: Comparative Analyses of Panicles and Roots in ‘Fusaotome’ and ‘Akitakomachi’

High temperatures during grain filling degrade rice quality, yet the metabolite-level basis of varietal tolerance—particularly root contributions—remains unclear. We compared the heat-tolerant ‘Fusaotome’ and the widely grown ‘Akitakomachi’ under control and high-temperature conditions. Panicles and roots were sampled at heading and profiled by capillary electrophoresis–mass spectrometry (CE–MS), followed by PCA, univariate testing, and KEGG pathway analysis. PCA resolved treatment and cultivar differences in an organ-specific manner. In panicles, ‘Fusaotome’ showed 8 increased metabolites (≥1.5-fold) and 11 decreased (≤1/1.5), whereas ‘Akitakomachi’ showed 19 increases and 6 decreases (p < 0.05). In roots, 12 metabolites increased in ‘Fusaotome’ and 9 in ‘Akitakomachi’; no significant decreases were detected. Pathway analysis indicated activation in ‘Fusaotome’ panicles of tryptophan, nicotinate/nicotinamide, arginine/proline, glycolysis/TCA, pyruvate, and vitamin B6 pathways, while ‘Akitakomachi’ emphasized phenylpropanoid, isoquinoline alkaloid, caffeine, and ubiquinone/terpenoid–quinone biosynthesis. In roots, ‘Fusaotome’ prioritized phenylalanine/phenylpropanoid, aromatic amino acids, lysine degradation, branched-chain amino acids, glycerophospholipids, and alkaloids, whereas ‘Akitakomachi’ favored nitrogen- and antioxidant-related routes. Collectively, the tolerant cultivar maintained antioxidant capacity and energy supply while coordinating root–panicle metabolism, whereas the susceptible cultivar shifted toward secondary defenses. These signatures nominate candidate metabolic markers and targets for breeding and management to stabilize rice production under warming climates.