Time-Series Multi-Omics Revealed Candidate Regulators of Antioxidant-Mediated Chilling Tolerance in Japonica Rice at Rice Booting Stage

Abstract

Chilling damage at the booting stage represents a primary constraint limiting stable yields of japonica rice in cold-growing regions, yet the molecular mechanisms driving genotypic variation in chilling tolerance is still unclear. In this study, the cold-tolerant cultivar Kongyu 131 and the cold-sensitive cultivar Longjing 11 were used as contrasting materials and subjected to low-temperature treatment at the booting stage for 0 h (T1), 72 h (T3), and 120 h (T5). The results showed that low-temperature was the dominant factor driving the divergence in yield traits between the two varieties: after T5 treatment, the seed setting rate (SSR) and grain weight per plant (GW) of KY131 were 16.76% and 38.96% higher than those of LJ11, respectively. Physiologically, KY131 maintained higher SOD, POD, and CAT activities and proline content throughout the treatment, with significantly lower accumulation of O2− and H2O2. Metabolomic profiling detected 101 differentially accumulated metabolites (DAMs) between cultivars, which were enriched in of fructose and mannose metabolism, amino sugar and nucleotide sugar metabolism, glycolysis/gluconeogenesis pathways. Notably, D-fructose 6-phosphate (Com_764_neg) was identified as a core DAM (VIP ≥ 1, p < 0.05) that accumulated to a greater extent in KY131 than in LJ11 under cold stress. Transcriptome analysis identified 692 differentially expressed genes (DEGs) between varieties, and integrated co-expression network and WGCNA analyses pinpointed OsbZIP69 (Os08g0549600) as the candidate hub transcription factor with the highest connectivity, which showed the strongest co-expression association the hexokinase OsHXK7 (Os05g0187100). The candidate OsbZIP69-OsHXK7 association and the core genes identified in this study provided a theoretical basis and gene resources for molecular breeding of cold-tolerant japonica rice in cold regions.