Transcriptomic profiling reveals stage-specific responses to cold stress in rice seedlings

Cold stress severely restricts rice growth, development, productivity, and geographical distribution. Here, we performed dynamic transcriptome profiling to investigate cold tolerance and cold-responsive metabolic pathways across distinct seedling growth stages in japonica rice cv. Nipponbare. We found that cold tolerance in Nipponbare seedlings exhibited a non-linear, V-shaped pattern: it gradually declined from 2 to 14 days after germination and then showed an upward trend from 16 to 24 days. Integrated analyses of RNA-seq, RT-qPCR, and physiological parameters indicated that 4-day seedlings primarily relied on a passive cold-resistance mode characterized by ‘low metabolism with high basal reserves’; 22-day seedlings adopted an active mode featuring ‘a strong antioxidant enzyme system with activation of secondary metabolism’; whereas 14-day seedlings represented a key transition stage marked by ‘growth-defense imbalance’. Collectively, our study elucidates seedling-age-dependent differences in cold tolerance and the corresponding metabolic regulatory mechanisms in Nipponbare, providing a theoretical basis for genetic improvement of cold tolerance in rice.