Introduction: As a type of biostimulant, protein hydrolysates (PHs) can promote crop growth, increase yield, and enhance crop tolerance to abiotic stresses. However, their application and research in rice production remain relatively limited. Methods: Focusing on“Lifenggu” (a soybean-derived protein hydrolysate), this study carried out multilocation field trials to evaluate the real-world application efficacy of this biostimulant on rice production across varying environmental conditions. Meanwhile, laboratory-based assays were conducted to analyze the doseresponse of rice growth to “Lifenggu” and its protective mechanisms under high-temperature and herbicide stress. Results: Field experimental results showed that “Lifenggu” could increase rice yield by 8.9%-14% (with an average increase of 10%). Physiological analysis revealed that “Lifenggu” might promote biomass accumulation by increasing the SPAD value of rice and enhancing the activity of nitrogen metabolic enzymes. Under herbicide and high-temperature stress, “Lifenggu” could alleviate the adverse effects caused by stress and reduce yield losses, possibly by increasing the activity of antioxidant enzymes and the content of proline, while decreasing the contents of malondialdehyde (MDA) and hydrogen peroxide (H2O2). Further transcriptomic analyses demonstrated that “Lifenggu” regulates the expression of genes involved in phytohormone biosynthesis, stress response pathways, and secondary metabolism. Discussion: This, in turn, serves as the molecular mechanism enabling its dual functions of promoting rice growth and improving stress tolerance. These results deepen insights into the yield-increasing effects of protein hydrolysates in rice, and offer both theoretical support and practical recommendations for their application in rice cultivation.

Dongxiang wild rice (DXWR, Oryza rufipogon Griff.), the northernmost known wild rice species, exhibits exceptional tolerance to combined low-temperature and anaerobic stress during seed germination, providing a unique model for understanding plant adaptation to complex environmental constraints. Here, we employed an integrated multi-omics approach combining genomic, transcriptomic, and metabolomic analyses to unravel the synergistic regulatory mechanisms underlying this tolerance. Genomic comparative analysis categorized DXWR genes into three evolutionary groups: 18,480 core genes, 15,880 accessory genes, and 6822 unique genes. Transcriptomic profiling identified 10,593 differentially expressed genes (DEGs) relative to the control, with combined stress triggering the most profound changes, specifically inducing the upregulation of 5573 genes and downregulation of 5809 genes. Functional characterization revealed that core genes, including DREB transcription factors, coordinate energy metabolism and antioxidant pathways; accessory genes, such as glycoside hydrolase GH18 family members, optimize energy supply via adaptive evolution; and unique genes, including specific UDP-glycosyltransferases (UDPGTs), confer specialized stress resilience. Widely targeted metabolomics identified 889 differentially accumulated metabolites (DAMs), highlighting significant accumulations of oligosaccharides (e.g., raffinose) to support glycolytic energy production and a marked increase in flavonoids (153 compounds identified, e.g., procyanidins) enhancing antioxidant defense. Hormonal signals, including jasmonic acid and auxin, were reconfigured to balance growth and defense responses. We propose a multi-level regulatory network based on a “core-unique-adaptive” genetic framework, centered on ERF family transcriptional hubs and coordinated through a metabolic adaptation strategy of “energy optimization, redox homeostasis, and growth inhibition relief”. These findings offer innovative strategies for improving rice stress tolerance, particularly for enhancing germination of direct-seeded rice under early spring low-temperature and anaerobic conditions, by utilizing key genes such as GH18s and UDPGTs, thereby providing crucial theoretical and technological support for addressing food security challenges under climate change.