Perspective: Twenty-five years of discovery and innovation on the plant circadian clock

In this Perspective article, Stacey Harmer reflects on plant gene regulation driven by the circadian cycle, using a thoughtful approachable tone to describe technological milestones that advanced our understanding of this complex mechanism of gene expression, as well as the work carried out by various laboratories over the past 25 years. Around the early 2000s, Arabidopsis thaliana became cemented as the primary model plant, as its genome had just been sequenced at that time. Only five clock genes had been identified in the species. The development of T-DNA collections, which facilitated access to mutant lines, together with the widespread use of DNA microarrays and the establishment of mathematical models, generated new insights and workflows in this research area. After 25 years, it is now clear that the circadian cycle regulates overall plant physiology through clock genes that function differently across tissues and even within individual cells within the same plant. To study differences in gene expression between individual cells, techniques such as single-cell RNA sequencing have emerged as the main available tools, enabling researchers to extend these studies to crop plants. Among the physiological processes affected by circadian clock genes are hormone signaling, stress responses, metabolism, and plant immune responses. The article concludes by highlighting the importance of understanding the circadian clock to address the challenges of crop adaptation under climate change. (Summary by Montserrat López-Coria). NPJ Biol Timing Sleep 10.1038/s44323-026-00076-2