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<p>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.</p>

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

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年4月1日

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

摘要

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.