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

<b>Background/Objectives:</b> Low-temperature stress during the grain-filling stage negatively affects rice grain quality and yield. Understanding the physiological and molecular mechanisms underlying cold tolerance is critical for breeding rice varieties with improved resilience. <b>Methods:</b> In this study, eight rice varieties with differential cold tolerance-LD1603, 13108, LD18, and 4-1021 (cold-tolerant) and LD3, LD4, LD121, and LD1604 (cold-sensitive)-were subjected to 17.5 °C 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. <b>Results:</b> 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 (<i>INV</i>, <i>SUS</i>, <i>HXK</i>, <i>FRK</i>, <i>amyA</i>, and <i>TPP</i>) 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 (<i>OsPAL04</i> and <i>OsCDPK7</i>) potentially involved in cold tolerance during grain filling. <b>Conclusions:</b> This study enhanced our understanding of the molecular response to low temperature during rice grain filling and provided candidate genes for developing cold-tolerant rice varieties through molecular breeding.