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

BACKGROUND: 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. RESULTS: 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). 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. CONCLUSIONS: The elucidated gene structure of TaCCA1 provides additional insight into the molecular basis of ambient temperature–dependent circadian regulation in wheat.