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The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana

Abstract

Light has an important role in modulating seedling growth and flowering time. We show that allelic variation at the PHYTOCHROME C (PHYC) photoreceptor locus affects both traits in natural populations of A. thaliana. Two functionally distinct PHYC haplotype groups are distributed in a latitudinal cline dependent on FRIGIDA, a locus that together with FLOWERING LOCUS C explains a large portion of the variation in A. thaliana flowering time1. In a genome-wide scan for association of 65 loci with latitude, there was an excess of significant P values, indicative of population structure. Nevertheless, PHYC was the most strongly associated locus across 163 strains, suggesting that PHYC alleles are under diversifying selection in A. thaliana. Our work, together with previous findings2,3,4,5, suggests that photoreceptor genes are major agents of natural variation in plant flowering and growth response.

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Figure 1: Identification of a defective PHYC allele in Fr-2.
Figure 2: Quantitative complementation analysis.
Figure 3: PHYC haplotypes.
Figure 4: Latitudinal cline of PHYC alleles.

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Acknowledgements

We thank the Nottingham Arabidopsis Stock Center for seed stocks of SALK T-DNA lines donated by J. Ecker and colleagues. We thank C. Lanz for help with sequencing, and K. Bomblies and Y.L. Guo for help with phylogenetic analysis. We thank K. Bomblies, V. Grbic, Y. Kobayashi, J. Lempe and S. Russell for discussion and critical reading of the manuscript. This work was supported by a European Molecular Biology Organization (EMBO) Long-Term Fellowship to S.B., a US National Institutes of Health (NIH) Postdoctoral Fellowship to T.P.M., an NIH grant (GM62932) to J.C. and D.W., and by the Max Planck Society, of which D.W. is a director. J.C. is a Howard Hughes Medical Institute (HHMI) Investigator.

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Correspondence to Detlef Weigel.

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Supplementary information

Supplementary Fig. 1

Markers used for mapping of the early flowering phenotype in Fr-2. (PDF 92 kb)

Supplementary Fig. 2

Flowering behavior of populations segregating for different PHYC alleles. (PDF 91 kb)

Supplementary Fig. 3

Latitudinal cline of PHYC alleles. (PDF 81 kb)

Supplementary Table 1

PHYC haplotypes of A. thaliana strains. (PDF 111 kb)

Supplementary Table 2

ANOVA of latitude by PHYC haplotype group interaction on residual variation in flowering time at 23 °C in short days after accounting for FRI functionality. (PDF 64 kb)

Supplementary Table 3

p-values obtained for different models testing for association with latitude (Latitude), FRI dependent interaction with latitude (Interaction), hypocotyl length under GA treatment (GAHypo) and total leaf number in short days (TLNSD) for 67 markers across 163 strains. (PDF 221 kb)

Supplementary Table 4

p-values obtained for two different models testing for latitudinal association with a completely independent set of markers across 56 strains. (PDF 204 kb)

Supplementary Table 5

Oligonucleotide primers. (PDF 68 kb)

Supplementary Table 6

Strains sequenced for PHYC. (PDF 87 kb)

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Balasubramanian, S., Sureshkumar, S., Agrawal, M. et al. The PHYTOCHROME C photoreceptor gene mediates natural variation in flowering and growth responses of Arabidopsis thaliana. Nat Genet 38, 711–715 (2006). https://doi.org/10.1038/ng1818

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