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

Yanting Li, Peng Zhang, Dianwei Yao, Ke Li, Tongyue Ouyang, Hao Li, Lihua Li, Jianqing Zhu, Xiaomei Jia, Xiaoying Ye, Jun Zhu & Rongjun Chen

BMC Plant Biology Volume 26, Article number 860 (2026)，01 April 2026（IF=4.8）

Abstract

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.