PLoS Biology (Oct 2022)

Circadian regulation of the transcriptome in a complex polyploid crop

  • Hannah Rees,
  • Rachel Rusholme-Pilcher,
  • Paul Bailey,
  • Joshua Colmer,
  • Benjamen White,
  • Connor Reynolds,
  • Sabrina Jaye Ward,
  • Benedict Coombes,
  • Calum A. Graham,
  • Luíza Lane de Barros Dantas,
  • Antony N. Dodd,
  • Anthony Hall

Journal volume & issue
Vol. 20, no. 10

Abstract

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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. This study presents a high-resolution circadian transcriptomic time-course dataset in wheat, revealing novel insights into the balance of circadian expression in a complex polyploid crop. Over 20% of genes in wheat are circadian regulated and a large proportion of triads exhibit unbalanced rhythmicity patterns.