Association analysis reveals genetic control underlying natural
variation in circadian rhythms in Arabidopsis
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.