A Multi-OmicApproach to Reveal the Effect of Low-Level Gamma Radiation on Rice Seeds

Importance of the Topic

The exposure of plants to ionizing radiation triggers complex biological responses that impact growth and yield. Low-level gamma radiation from Fukushima soil contamination presents a unique case to study seed-level adaptations. A multi-omic analysis combining transcriptome and metabolome profiling offers insights into molecular mechanisms underlying radiation stress in rice seeds.

Objectives and Study Overview

This study aims to characterize the effects of chronic low-dose gamma radiation on rice seeds harvested from contaminated fields in Fukushima Prefecture. By comparing irradiated seeds with controls grown in uncontaminated soils, the research integrates gene expression and metabolic profiling to identify radiation-responsive pathways and biomarkers.

Methodology

• Sample Collection and Preparation: Rice seeds were harvested, dehusked, flash frozen, and stored at −80 °C. RNA and metabolites were extracted from powdered seed samples.
• Transcriptome Profiling: Total RNA integrity was checked on an Agilent Bioanalyzer. Labelled cRNA was hybridized to Agilent rice 4×44 k microarrays. Data were processed with Agilent Feature Extraction and GeneSpring software, using a moderated t-test with FDR correction (p<0.05, fold change >2).
• Metabolome Profiling: Polar and nonpolar metabolites were extracted using a chloroform:methanol:water method. Derivatized samples were analyzed on an Agilent 7200 GC/Q-TOF and an Agilent 1290 LC coupled to a 6550 Q-TOF. Data were processed with MassHunter and matched to the Agilent-Fiehn library.
• Data Integration: Differential genes and metabolites were mapped to pathways using GeneSpring/Mass Profiler Professional. Combined analysis identified overlapping signatures in defense, cell wall, fatty acid, and antioxidant pathways.

Used Instrumentation

• Agilent 2100 Bioanalyzer with RNA 6000 Nano chips
• Agilent SureScan Microarray Scanner
• Agilent 7200 Series GC/Q-TOF
• Agilent 1290 Infinity LC System with 6550 Q-TOF

Main Results and Discussion

A total of 2 331 genes and 383 metabolites were differentially regulated in irradiated seeds. Key findings include:

• Upregulation of stress-related metabolites such as L-proline, L-alanine, raffinose, and 12-OPDA.
• Downregulation of amino acids like L-arginine and L-methionine, indicating metabolic rerouting.
• Activation of phenylpropanoid biosynthesis, fatty acid metabolism, glutathione and peroxisome pathways, highlighting defense and energy cycling.

These molecular alterations suggest a coordinated response to mitigate radiation-induced damage.

Benefits and Practical Applications

The identified gene and metabolite markers can serve as radio-responsive biomarkers for seed quality assessment. Insights into defense pathways support strategies to enhance crop resilience under environmental stress and inform agricultural QA/QC protocols.

Future Trends and Potential Applications

Expanding multi-omic integration to include proteomics and ionomics will deepen understanding of stress networks. Field-deployable diagnostics and marker-assisted breeding could leverage these signatures for crop improvement and environmental monitoring.

Conclusion

The combined transcriptomic and metabolomic approach revealed that rice seeds exposed to chronic low-dose gamma radiation activate a well-coordinated defense mechanism involving key metabolic pathways. The study demonstrates the power of integrated omics to uncover complex stress responses.

Reference

• Hayashi G, Shibato J, Kubo A, et al. Unraveling low-level gamma radiation-responsive changes in expression of early and late genes in leaves of rice seedlings at Iitate village, Fukushima. J Hered. 2014;105:723–738.