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Abstract

Light plays a major role in several aspects of plant development including seedling growth and floral transition. Wild strains of Arabidopsis thaliana show extensive phenotypic variation in both these responses. Quantitative trait locus (QTL) mapping studies and subsequent molecular genetic analysis have identified several loci that contribute natural variation in flowering and light responses. However, most of the identified natural alleles are specific to strains and/or phenotypes. Here we report that common alleles of the photoreceptor gene PHYC confer natural phenotypic variation in both flowering time as well as seedling growth across wild strains of A. thaliana. We show that the short day early flowering phenotype of the Fr-2 strain is due to a naturally occurring loss-of-function allele of PHYC. In addition, quantitative complementation suggest that the commonly used laboratory strain Ler carries a weak allele of PHYC. Sequence analysis, haplotype tagging, phenotypic association and a comparison of available QTL maps reveal two functionally distinct haplogroups of PHYC that could account for flowering time and light sensitivity QTLs detected across several RIL populations. The PHYC haplogroups display a FRIGIDA-dependent latitudinal cline in their distribution that is stronger than what is reported for FLOWERING LOCUS C. A genomic scan with 67 SNPs with matching allele frequency with of that of PHYC across 165 eurasian strains reveals an excess of significant p-values indicating population structure. Nevertheless, PHYC is ranked the highest among the 67 SNPs for association with latitude indicating the PHYC haplogroups are under diversifying selection in A.thaliana. Our analysis together with previous findings suggests the photoreceptor genes to be major agents for local adaptation in A. thaliana.