Transcriptomic Dynamics of Rice Varieties with Differential Cold Tolerance During Grain Filling Stage Under Low-Temperature Stress

Low-temperature stress during the grain-filling stage negatively affects rice grain quality and yield. Understanding physiological and molecular mechanisms underlying cold tolerance is critical for breeding rice varieties with improved resilience.In this study, eight rice varieties with differential cold tolerance (LD1603, 13108, LD18, and 4-1021 as cold-tolerant; LD3, LD4, LD121, and LD1604 as cold-sensitive) were subjected to 17.5 degrees Celsius low-temperature stress during grain filling in a naturally illuminated phytotron. Amylose and protein content, as well as taste quality, were analyzed. RNA-sequencing was performed to identify differentially expressed genes and transcription factors associated with cold response.Under low-temperature stress, amylose and protein content significantly increased in all eight varieties. The taste quality of cold-sensitive varieties declined markedly, whereas cold-tolerant varieties maintained higher and more stable taste quality values. Transcriptomic analysis revealed that key enzyme genes (_INV_, _SUS_, _HXK_, _FRK_, _amyA_, and _TPP_) in the starch and sucrose metabolism pathway were significantly upregulated in cold-tolerant varieties (LD18 and 4-1021), but suppressed in cold-sensitive varieties. Several cold-responsive transcription factors from the _NAC_, _WRKY_, _AP2/ERF_, _MYB_, and _bZIP_ families were also identified. Weighted Gene Co-expression Network Analysis (WGCNA) further revealed hub TFs (_OsWRKY1_, _OsWRKY24_, _OsWRKY53_, and _OsMYB4_) and structural genes (_OsPAL04_ and _OsCDPK7_) potentially involved in cold tolerance during grain filling.This study enhances our understanding of the molecular response to low temperature during rice grain filling and provides candidate genes for developing cold-tolerant rice varieties through molecular breeding.