Low-temperature-specific effects of PHYTOCHROME C on the circadian clock in Arabidopsis suggest that PHYC underlies natural variation in biological timing

The circadian clock is a fundamental feature of gene regulation and cell physiology in eukaryotes and some prokaryotes, and an exemplar gene regulatory network in Systems Biology. The circadian system in Arabidopsis thaliana is complex in part due to its photo-transduction pathways. Analysis of natural genetic variation between Arabidopsis accessions Cape Verde Islands (Cvi-0) and Landsberg erecta (Ler) identified a major, temperature-specific Quantitative Trait Locus (QTL) on chromosome V that altered the circadian period of leaf movement (Edwards et al., Genetics, 2005). We tested Near-Isogenic Lines (NILs) to confirm that Ler alleles at this PerCv5c QTL lengthened the circadian period at 12°C, with little effect at higher temperatures. The PHYTOCHROME C gene lies within the QTL interval, and contains multiple sequence variants. Plants carrying either a T-DNA-insertion into PHYC or a deletion of PHYC also lengthened circadian period under white light, except at 27°C. phyB and phyABE mutants lengthened period only at 12°C. These results extend recent data showing PhyC effects in red light, confirming the number of photoreceptor proteins implicated in the plant circadian system at eleven. The connection between light input mechanisms and temperature effects on the clock is reinforced. Natural genetic variation within PHYC is likely to underlie the PerCv5c QTL. Our results suggest that functional variation within the PHYC-Ler haplotype group might contribute to the evolution of the circadian system and possibly to clock-related phenotypes such as flowering time. These results have previously passed peer-review, so we provide them in this citable preprint.