genomic analysis of the shade avoidance response in arabidopsis

• Published in: Plant physiology (Bethesda) Vol. 133; no. 4; pp. 1617 - 1629
• Main Authors: Devlin, P.F, Yanovsky, M.J, Kay, S.A
• Format: Journal Article
• Language: English
• Published: Rockville, MD American Society of Plant Biologists 01-12-2003; American Society of Plant Physiologists
• Subjects: Arabidopsis - genetics; Arabidopsis - growth & development; Arabidopsis - radiation effects; Arabidopsis thaliana; Base Sequence; Biological and medical sciences; Cell physiology; Darkness; Down regulation; Focus Issue on Light Signaling; Fundamental and applied biological sciences. Psychology; Gene expression; Gene expression regulation; Gene Expression Regulation, Plant - genetics; gene overexpression; Genes; Genome, Plant; Hypocotyls; Light; microarray technology; Molecular and cellular biology; mutants; Nucleic Acid Hybridization; Oligonucleotide Array Sequence Analysis; P values; photoreceptors; Phototropism - genetics; phyA protein; phyB protein; phytochrome; Plant growth. Development of the storage organs; Plant physiology and development; plant proteins; plant response; plant stress; Plants; promoter regions; Promoter Regions, Genetic - genetics; Seedlings; shade; Signal transduction; Transcription factors; Up regulation; Vegetative apparatus, growth and morphogenesis. Senescence; Vision, photoreception; Light effect; Transcription promoter; Genetic variant; Photoreceptor; Phototropism; Shading; Gene expression; Genetic determinism; Growth habit; Photomorphogenesis; Morphogenesis; Arabidopsis thaliana; Signal transduction; Cruciferae; Dicotyledones; Light; Angiospermae; Phytochrome; Spermatophyta; Intraspecific comparison; Experimental plant; Genome
• ISSN: 0032-0889; 1532-2548
• DOI: 10.1104/pp.103.034397

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.