First published online November 26, 2003; 10.1104/pp.103.034397
Plant Physiology 133:1617-1629 (2003)
© 2003 American Society of Plant Biologists
A Genomic Analysis of the Shade Avoidance Response in Arabidopsis1,[w]
Paul Francis Devlin2,3,
Marcelo Javier Yanovsky2,4 and
Steve A. Kay*
The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
Plants respond to the proximity of neighboring vegetation by elongating to prevent shading. Red-depleted light reflected from neighboring vegetation triggers a shade avoidance response leading to a dramatic change in plant architecture. These changes in light quality are detected by the phytochrome family of photoreceptors. We analyzed global changes in gene expression over time in wild-type, phyB mutant, and phyA phyB double mutant seedlings of Arabidopsis in response to simulated shade. Using pattern fitting software, we identified 301 genes as shade responsive with patterns of expression corresponding to one of various physiological response modes. A requirement for a consistent pattern of expression across 12 chips in this way allowed more subtle changes in gene expression to be considered meaningful. A number of previously characterized genes involved in light and hormone signaling were identified as shade responsive, as well as several putative, novel shade-specific signal transduction factors. In addition, changes in expression of genes in a range of pathways associated with elongation growth and stress responses were observed. The majority of shade-responsive genes demonstrated antagonistic regulation by phyA and phyB in response to shade following the pattern of many physiological responses. An analysis of promoter elements of genes regulated in this way identified conserved promoter motifs potentially important in shade regulation.
Article, publication date, and citation information can be found at http://www.plantphysiol.org/cgi/doi/10.1104/pp.103.034397.
1 This work was supported by the National Institutes of Health (grant no. GM56006), by the Torrey Mesa Research Institute (funding to S.A.K.), by EMBO (long-term fellowship to P.F.D.), and by Pew Charitable Trusts (fellowship to M.J.Y.). This is manuscript no. 15909–CB of The Scripps Research Institute.
[w] The online version of this article contains Web-only data.
2 These authors contributed equally to the paper.
3 Present address: Department of Life Sciences, King's College London, 150 Stamford Street, London SE1 9NN, UK.
4 Present address: Catedra Fisiología Vegetal, Facultad de Agronomia, Universidad de Buenos Aires, Av. San Martin 4453, C1417DSQ, Buenos Aires, Argentina.
* Corresponding author; e-mail stevek{at}scripps.edu; fax 858–784–2973.
Received October 6, 2003;
returned for revision October 13, 2003;
accepted October 15, 2003.
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