biostudies-literatureChowdhury NBNational Institute of Food and AgricultureNational Science Foundation16432https://www.ebi.ac.uk/biostudies/studies/S-EPMC12069599biostudies-literatureUnknown15(1)Rising temperatures due to global warming can negatively impact rice grain quality and yield. This study investigates the effects of increased warmer night temperatures (WNT), a consequence of global warming, on the quality of rice kernel, particularly grain chalkiness. By integrating computational and experimental approaches, we used a rice grain metabolic network to discover the metabolic factors of chalkiness. For this, we reconstructed the rice grain genome-scale metabolic model (GSM), iOSA3474-G and incorporated transcriptomics data from three different times of the day (dawn, dawn 7 h, and dusk) for both control and WNT conditions with iOSA3474-G. Three distinct growth phases: anoxia, normoxia, and hyperoxia, were identified in rice kernels from the GSMs, highlighting the grain-filliScientific reportsTranscriptome enhanced rice grain metabolic model identifies histidine level as a marker for grain chalkiness.PMC120695992024-67013-423851943310Saha RChandran AKNWalia HChowdhury NBfalseTranscriptome enhanced rice grain metabolic model identifies histidine level as a marker for grain chalkiness.Rising temperatures due to global warming can negatively impact rice grain quality and yield. This study investigates the effects of increased warmer night temperatures (WNT), a consequence of global warming, on the quality of rice kernel, particularly grain chalkiness. By integrating computational and experimental approaches, we used a rice grain metabolic network to discover the metabolic factors of chalkiness. For this, we reconstructed the rice grain genome-scale metabolic model (GSM), iOSA3474-G and incorporated transcriptomics data from three different times of the day (dawn, dawn 7 h, and dusk) for both control and WNT conditions with iOSA3474-G. Three distinct growth phases: anoxia, normoxia, and hyperoxia, were identified in rice kernels from the GSMs, highlighting the grain-filli2025-01-01T00:00:00Z2025 May2026-06-02T21:04:35.809Z2026-04-20T03:14:32.466ZS-EPMC120695994035548210.1038/s41598-025-00504-6