CIRCADIAN CLOCK ASSOCIATED 1 Expression Responds to High Temperature Precisely Through Alternative Splicing in Arabidopsis

The circadian clock enables plants to adapt to ambient temperature fluctuations. In Arabidopsis thaliana, CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) generates distinct isoforms via alternative splicing (AS), but how this mediates clock stability under high temperature (HT) remains unclear. Here, we show that CCA1 precisely discriminates HT gradients through AS: under moderate HT (28°C-37°C), CCA1βab isoforms (CCA1βa/βb) are upregulated, with CCA1βb specifically accumulating at 37°C, while CCA1α remains stable; at extreme HT (42°C), CCA1 is globally upregulated without isoform specificity. The HT response of CCA1 is time-dependent, CCA1βab is transiently induced around dawn, whereas CCA1α exhibits delayed, AS-dependent upregulation with thermal memory to anticipate subsequent HT. Tissue-specific AS was observed, with CCA1α upregulated in roots/stems but downregulated in shoots/flowers under HT. Notably, the temperature-dependent shift in the CCA1βa-to-CCA1βb isoform ratio is involved in fine-tuning plant defense against biotic stresses and coordinating reactive oxygen species homeostasis. Our findings uncover a sophisticated regulatory network where CCA1 integrates temperature signals via AS, ensuring plant adaptation to thermal fluctuations while preserving circadian stability.