Shade avoidance components and pathways in adult plants revealed by phenotypic profiling

PLoS Genet. 2015 Apr 15;11(4):e1004953. doi: 10.1371/journal.pgen.1004953. eCollection 2015 Apr.


Shade from neighboring plants limits light for photosynthesis; as a consequence, plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light. Collectively the response to foliar shade is called the shade avoidance syndrome (SAS). The SAS includes elongation of a variety of organs, acceleration of flowering time, and additional physiological responses, which are seen throughout the plant life cycle. However, current mechanistic knowledge is mainly limited to shade-induced elongation of seedlings. Here we use phenotypic profiling of seedling, leaf, and flowering time traits to untangle complex SAS networks. We used over-representation analysis (ORA) of shade-responsive genes, combined with previous annotation, to logically select 59 known and candidate novel mutants for phenotyping. Our analysis reveals shared and separate pathways for each shade avoidance response. In particular, auxin pathway components were required for shade avoidance responses in hypocotyl, petiole, and flowering time, whereas jasmonic acid pathway components were only required for petiole and flowering time responses. Our phenotypic profiling allowed discovery of seventeen novel shade avoidance mutants. Our results demonstrate that logical selection of mutants increased success of phenotypic profiling to dissect complex traits and discover novel components.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cyclopentanes / metabolism
  • Flowers / physiology
  • Genes, Plant
  • Indoleacetic Acids / metabolism
  • Magnoliopsida / genetics*
  • Magnoliopsida / metabolism
  • Magnoliopsida / physiology
  • Metabolic Networks and Pathways*
  • Mutation
  • Oxylipins / metabolism
  • Phenotype*
  • Phototropism / genetics*
  • Plant Leaves / physiology
  • Seeds / physiology
  • Sunlight


  • Cyclopentanes
  • Indoleacetic Acids
  • Oxylipins
  • jasmonic acid

Associated data

  • GEO/GSE66967

Grants and funding

We acknowledge financial support of National Science Foundation Integrative Organismal Systems (; IOS-0923752) and United States Department of Agriculture USDA NIFA project (; CA-D-PLB-7226-H) to JNM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.