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Rees, Hannah, Rusholme-Pilcher, Rachel, Bailey, Paul, Colmer, Joshua, White, Benjamen, Reynolds, Connor, Ward, Sabrina Jaye, Coombes, Benedict, Graham, Calum A., de Barros Dantas, Luíza Lane, Dodd, Antony N. and Hall, Anthony 
ORCID: https://orcid.org/0000-0002-1806-020X
(2022)
Circadian regulation of the transcriptome in a complex polyploid crop.
PLoS Biology, 20 (10).
ISSN 1544-9173
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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.
| Item Type: | Article |
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| Additional Information: | Data Availability Statement: Data for the recreation of all main figures in this manuscript are available in S1 Data. Data for the recreation of all supplementary figures in this manuscript are available in S2 Data. Fastq data from the RNA-seq circadian time course are available to view from the Grassroots Data Repository: https://opendata.earlham.ac.uk/opendata/data/wheat_circadian_Rees_2021. A summary csv table with expression of wheat genes (TPM), Metacycle estimates, gene annotations and triad balance classification can be viewed in S11 Table is available here: https://opendata.earlham.ac.uk/opendata/data/wheat_circadian_Rees_2021. A TPM expression matrix at the individual replicate level with triad IDs information is also available: S12 Table: https://opendata.earlham.ac.uk/opendata/data/wheat_circadian_Rees_2021. Code for creating Loom plots, the cross-correlation analysis and the clustering analysis are available from our groups GitHub repository: https://github.com/AHallLab/circadian_transcriptome_regulation_paper_2022/tree/main. Funding Information: H.R., R.R.P. and A.H. were funded by the BBSRC Core Strategic Programme Grant (Genomes to Food Security) BB/CSP1720/1 and its constituent work package, BBS/E/T/000PR9819 (WP2 Regulatory interactions and Complex Phenotypes). B.W., R.R.P. and A.H. was supported by the BBSRC Designing Future Wheat grant BB/ P016855/1; BBS/E/T/000PR9783 (DFW WP4 Data Access and Analysis). B.C and J.C were supported by the BBSRC funded Norwich Research Park Biosciences Doctoral Training Partnership grant BB/M011216/1. C.R. by a BBSRC grant BB/ V509267/1 and Wave 1 of The UKRI Strategic Priorities Fund under the EPSRC Grant EP/ T001569/1, particularly the "AI for Science" theme within that grant & The Alan Turing Institute. We would also like to acknowledge BBS/E/T/ 000PR9816 (NC1 - Supporting EI's ISPs and the UK Community with Genomics and Single Cell Analysis) for data generation and BB/CCG1720/1 for the physical HPC infrastructure and data centre delivered via the NBI Computing infrastructure for Science (CiS) group. P.B. was supported by a BBSRC TRDF grant BB/N023145/1. A.N.D., L.L.B. D. and C.A.G. are funded by BBSRC ISP Genes in the Environment (BB/P013511/1). C.A.G. was also funded by UK BBSRC SWBIO DTP (BB/M009122/ 1). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. © 2022 Rees et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
| Uncontrolled Keywords: | neuroscience(all),biochemistry, genetics and molecular biology(all),immunology and microbiology(all),agricultural and biological sciences(all) ,/dk/atira/pure/subjectarea/asjc/2800 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 31 Oct 2024 15:30 |
| Last Modified: | 01 Nov 2024 11:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97389 |
| DOI: | 10.1371/journal.pbio.3001802 |
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