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Association analysis reveals genetic control underlying natural variation in circadian rhythms in Arabidopsis
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  • Hannah Rees,
  • Ryan Joynson,
  • James Brown,
  • Antony Hall
Hannah Rees
Earlham Institute
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Ryan Joynson
Earlham Institute
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James Brown
John Innes Centre
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Antony Hall
Earlham Institute
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Abstract

Circadian clocks have evolved to resonate with external day and night cycles. However, these entrainment signals are not consistent everywhere and vary with latitude, climate and seasonality. This leads to divergent selection for clocks which are locally adapted. To investigate the genetic basis for this circadian variation, we used a Delayed Fluorescence (DF) imaging assay to screen 191 naturally occurring Swedish Arabidopsis accessions for their circadian phenotypes. We demonstrate that period length co-varies with both geography and population sub-structure. Several candidate loci linked to period, phase and Relative Amplitude Error (RAE) were revealed by genome-wide association mapping and candidate genes were investigated using TDNA mutants. We show that natural variation in a single non-synonymous substitution within COR28 is associated with a long-period and late-flowering phenotype similar to that seen in TDNA knock-out mutants. COR28 is a known coordinator of flowering time, freezing tolerance and the circadian clock; all of which may form selective pressure gradients across Sweden. We demonstrate the effect of the COR28-58S SNP in increasing period length through a co-segregation analysis. Finally, we show that period phenotypic tails remain diverged under lower temperatures and follow a distinctive ‘arrow-shaped’ trend indicative of selection for a cold-biased temperature compensation response.

Peer review status:ACCEPTED

29 Sep 2020Submitted to Plant, Cell & Environment
30 Sep 2020Submission Checks Completed
30 Sep 2020Assigned to Editor
02 Oct 2020Reviewer(s) Assigned
18 Oct 2020Review(s) Completed, Editorial Evaluation Pending
19 Oct 2020Editorial Decision: Revise Minor
21 Oct 20201st Revision Received
22 Oct 2020Submission Checks Completed
22 Oct 2020Assigned to Editor
22 Oct 2020Reviewer(s) Assigned
02 Nov 2020Review(s) Completed, Editorial Evaluation Pending
02 Nov 2020Editorial Decision: Revise Minor
05 Nov 20202nd Revision Received
06 Nov 2020Submission Checks Completed
06 Nov 2020Assigned to Editor
06 Nov 2020Review(s) Completed, Editorial Evaluation Pending
06 Nov 2020Editorial Decision: Accept