Molecular genetic examination of Circadian Clock Associated 1 gene (CCA1) in hexaploid wheat

The circadian clock is one of the most crucial regulatory pathways controlling plant development and stress responses, with the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) gene playing a central role. While the regulatory mechanisms and structure of this gene have been well characterized in Arabidopsis thaliana L., only limited information is available for hexaploid wheat. The daily expression of TaCCA1, measured as the combined transcript abundance across the three wheat subgenomes, showed a clear diurnal rhythm in all three winter wheat genotypes, and this rhythm was significantly modulated by ambient temperature. In the early-heading genotype, the peak expression estimated by the cosinor model was approximately threefold higher at 18 °C than at 25 °C (p < 1 × 10− 15, respectively). We identified a substantially larger insertion in intron 3 of CCA1 gene in barley, which is even longer in hexaploid wheat compared with the homologous region in Arabidopsis. Phylogenetic analysis of CCA1 gene revealed a strong association between the subgroups and genomes of the studied species. An alternative isoform located in intron 6 of LATE ELONGATED HYPOCOTYL (LHY) gene in barley showed 95% similarity to a sequence found in intron 3 of TaCCA1. We also identified a low-temperature–responsive cis-regulatory motif in hexaploid wheat that was detected exclusively in the A subgenome and was highly conserved. The elucidated gene structure of TaCCA1 provides additional insight into the molecular basis of ambient temperature–dependent circadian regulation in wheat.