Speed breeding represents a pivotal technology for enhancing crop breeding efficiency. This study systematically examined the regulation of LED light environments, planting density, and gibberellic acid (GA₃) on rice growth cycle progression in plant factories, establishing an integrated speed breeding protocol. The experimental design comprised three components: (1) coupling seedling age (9–25 days, variety-dependent) with LED environments and planting densities (25–100 plants/tray); (2) combining light intensity gradients (450 and 900 μmol·m⁻²·s⁻¹) with photoperiod control; (3) applying GA₃ gradients (0–120 ppm) to enhance immature seed germination. Results indicated that high planting densities (>50 plants/tray) prolonged the growth cycle and decreased yield, whereas 25 plants/tray optimally balanced growth cycle shortening and yield maximization. Under short-day induction, Nipponbare (Nip) and Wufeng B (WFB) reached heading at 39 and 58 days after sowing (DAS), respectively. Stage-specific light responses were observed: 450 μmol·m⁻²·s⁻¹ during the basic vegetative phase (BVP) promoted morphological development, whereas 900 μmol·m⁻²·s⁻¹ during the photoperiod-sensitive phase (PSP) accelerated tillering and panicle differentiation. GA₃ treatment (60 ppm) enhanced the germination rate of immature seeds by 31%. The optimized lightregimes comprised natural light + 900 μmol·m⁻²·s⁻¹ (NL–900) and 450 μmol·m⁻²·s⁻¹ + 900 μmol·m⁻²·s⁻¹ (450–900), combined with density control (25 plants/tray) and GA₃-mediated immature seed utilization, shortened the generation time to 54 days and 70 days for Nip and WFB, respectively. This integrated protocol establishes an efficient strategy for rice speed breeding in plant factories.

Rice is a short-day thermophilic crop that originated from the low latitudes of the tropics and subtropics; it requires high temperatures for growth but is sensitive to low temperatures. Therefore, it is highly important to explore and analyze the molecular mechanism of cold tolerance in rice to expand rice planting areas. Here, we report a phenotypic evaluation based on low-temperature stress in indica rice (R998) and wild rice (GZW) and a comparative transcriptomic study conducted at six time points. After 7 days of low-temperature treatment at 10 °C, R998 exhibited obvious yellowing and greening of the leaves, while GZW exhibited high low-temperature resistance, and the leaves maintained their normal morphology and exhibited no yellowing; GZW has a higher survival rate. Principal component analysis (PCA) and cluster analysis of the RNA-seq data revealed that the difference in low-temperature resistance between the two cultivars was caused mainly by the difference in low-temperature treatment after 6 h. Differential expression analysis revealed 2615 unique differentially expressed genes (DEGs) in the R998 material, 1578 unique DEGs in the GZW material, 1874 unique DEGs between R998 and GZW, and 2699 DEGs that were differentially expressed not only between cultivars but also at different time points in the same material under low-temperature treatment. A total of 15,712 DEGs were detected and were significantly enriched in the phenylalanine metabolism, photosynthesis, plant hormone signal transduction, and starch and sucrose metabolism pathways. These 15,712 DEGs included 1937 genes encoding transcription factors (TFs), of which 10 have been identified with functional validation in previous studies. In addition, a gene regulatory network was constructed via weighted gene correlation network analysis (WGCNA), and 12 key genes related to low-temperature tolerance in rice were identified, including five genes encoding TFs, one of which was identified and verified in previous studies. These results provide a theoretical basis for an in-depth understanding of the molecular mechanism of low-temperature tolerance in rice and provide new genetic resources for the study of low-temperature tolerance in rice.