Transcriptome enhanced rice grain metabolic model identifies histidine level as a marker for grain chalkiness

Area of Science:

• Plant Science
• Metabolic Engineering
• Climate Change Biology

Background:

• Global warming causes rising temperatures, negatively impacting rice grain quality and yield.
• Warmer night temperatures (WNT) are a significant consequence of global warming affecting rice quality, particularly grain chalkiness.

Purpose of the Study:

• To investigate the effects of WNT on rice kernel quality, focusing on grain chalkiness.
• To identify metabolic factors and regulators contributing to rice grain chalkiness under WNT using integrated computational and experimental approaches.

Main Methods:

• Reconstruction of a rice grain genome-scale metabolic model (GSM), iOSA3474-G.
• Integration of transcriptomics data from control and WNT conditions across different times of day.
• Analysis of metabolic flux and bottleneck analysis to identify key regulators and growth phases (anoxia, normoxia, hyperoxia).

Main Results:

• Identified three distinct growth phases in rice kernels (anoxia, normoxia, hyperoxia) linked to oxygen levels.
• Proposed histidine as a marker for normoxia (associated with chalkiness) and tyrosine for hyperoxia.
• Identified nucleoside diphosphate kinase as a central metabolic regulator and suggested a link between monodehydroascorbate reductase and hyperoxia.

Conclusions:

• Findings provide targeted insights into the metabolic network governing rice grain chalkiness under WNT.
• Integration of GSM and transcriptomics enhances understanding of environmental factors, metabolism, and grain quality.
• Identified potential markers for developing climate-resilient rice varieties.