Circadian regulation of the transcriptome in a complex polyploid crop
Hannah Rees, Rachel Rusholme‐Pilcher, Paul Bailey, Joshua Colmer, Benjamen White, Connor Reynolds, Ben J. Ward, Benedict Coombes, Calum A. Graham, Luíza Lane de Barros Dantas, Antony N. Dodd, Anthony Hall
Abstract
The circadian clock is a finely balanced timekeeping mechanism that coordinates programmes of gene expression. It is currently unknown how the clock regulates expression of homoeologous genes in polyploids. Here, we generate a high-resolution time-course dataset to investigate the circadian balance between sets of 3 homoeologous genes (triads) from hexaploid bread wheat. We find a large proportion of circadian triads exhibit imbalanced rhythmic expression patterns, with no specific subgenome favoured. In wheat, period lengths of rhythmic transcripts are found to be longer and have a higher level of variance than in other plant species. Expression of transcripts associated with circadian controlled biological processes is largely conserved between wheat and Arabidopsis; however, striking differences are seen in agriculturally critical processes such as starch metabolism. Together, this work highlights the ongoing selection for balance versus diversification in circadian homoeologs and identifies clock-controlled pathways that might provide important targets for future wheat breeding.