Rice is a staple food for over half of the global population, and the postharvest quality deterioration of paddy rice is closely linked to lipid degradation. Low-temperature storage represents an effective strategy for maintaining rice quality and achieving green storage. However, the intrinsic mechanisms by which prolonged low-temperature storage coordinately regulates rice lipid metabolism at the level of metabolite dynamics and gene expression networks to maintain its stability have not been fully elucidated.

This study aimed to integrate multi-omics technologies to systematically elucidate biochemical and molecular mechanisms underlying lipid stability in japonica rice during long-term low-temperature storage.

Fresh Nanjing 46 paddy rice was stored at 25 and 15 ℃ for 360 days, with sampling every 30 days. An integrated approach combining physiological and biochemical analyses, lipidomics, and transcriptomics was employed to systematically investigate stabilization mechanisms.

Low-temperature storage effectively maintained rice lipid stability through a multi-layered regulatory network. Regarding membrane lipid metabolism, low-temperature storage downregulated PLDα1, thereby delaying the hydrolysis of phospholipids, including phosphatidylethanolamine, phosphatidylinositol, and phosphatidylcholine, and helping to maintain cellular membrane integrity. Additionally, reduced expression of OsCDase limited sphingolipid degradation, further enhancing plasma membrane stability. In terms of lipid hydrolysis, lipase activity was suppressed under low-temperature conditions, inhibiting triglyceride hydrolysis. In oxidative metabolic pathways, the downregulation of OsFAD2 and ACX1 genes inhibited polyunsaturated fatty acid synthesis and β-oxidation, thus alleviating oxidative stress. Reduced lipoxygenase (LOX，Lipoxygenase) activity at low temperatures further mitigated the oxidation of unsaturated fatty acids, thereby minimizing off-flavor formation.

During rice storage, lipid hydrolysis served as a critical precursor to oxidation, with both processes jointly determining quality deterioration. Low-temperature storage simultaneously inhibited lipid hydrolysis and oxidation pathways, consequently maintaining lipid compositional stability at the metabolomic level and delaying quality decline at the phenotypic level.

Rice grain undergoes various physiological and biochemical changes during long-term storage, impacting both stability and quality. Those factors contribute to rice grain quality deterioration during its storage stage, such as lipid oxidation, starch degradation, protein modifications, membrane homeostasis imbalance, and oxidative stress collectively. However, the molecular mechanisms underlying these changes remain elusive.

This study aimed to analyze differentially expressed genes (DEGs) in stored rice grian, construct a co-expression network, identify core genes using WGCNA and explore regulatory mechanisms associated with rice storage stability.

Transcriptomic analysis was conducted on Japonica rice (Nanjing 46) grain stored for different durations (0, 3, 6, 9 and 12 months) to obtain gene expression profiles. WGCNA was employed to identify highly variable genes during storage, construct a weighted gene co-expression network, and identify storage-time-specific modules. Core genes screening was based on network connectivity, followed by functional enrichment analysis and physiological and biochemical assays to explore their potential roles in storage quality regulation.

A total of 9 050 DEGs were identified, with 8 654 showing variations across storage stages, and 396 were expressed consistently across all time points. WGCNA identified 17 gene co-expression modules, of which four showed strong associations with storage duration. Connectivity analysis further highlighted key genes with regulatory potential：OsOLE4 and OsCDAP3, involved in lipid metabolism; OsLEA32, OsAGP24 and OsRHD3 associated with maintaining cellular stability; OsERF064 linked to the ethylene signaling pathway and OsEMF2a, an epigenetic regulator. Additionally, five candidate genes lacking functional annotation were identified for further study.

This study systematically analyzed the molecular regulatory network of rice grain storage using transcriptomics and WGCNA, revealing that rice grain adapts to storage environments through multi-level gene regulatory mechanisms. Core genes within specific modules played pivotal roles in antioxidant activity, nutrient metabolism, membrane stability, and cellular function maintenance. These findings provided a biological basis for delaying rice quality deterioration and offered potential genetic resources for improving rice grain storage stability.