Molecular characterization of the submergence response of the Arabidopsis thaliana ecotype Columbia

New Phytol. 2011 Apr;190(2):457-71. doi: 10.1111/j.1469-8137.2010.03590.x. Epub 2011 Jan 13.


• A detailed description of the molecular response of Arabidopsis thaliana to submergence can aid the identification of genes that are critical to flooding survival. • Rosette-stage plants were fully submerged in complete darkness and shoot and root tissue was harvested separately after the O(2) partial pressure of the petiole and root had stabilized at c. 6 and 0.1 kPa, respectively. As controls, plants were untreated or exposed to darkness. Following quantitative profiling of cellular mRNAs with the Affymetrix ATH1 platform, changes in the transcriptome in response to submergence, early darkness, and O(2)-deprivation were evaluated by fuzzy k-means clustering. This identified genes co-regulated at the conditional, developmental or organ-specific level. Mutants for 10 differentially expressed HYPOXIA-RESPONSIVE UNKNOWN PROTEIN (HUP) genes were screened for altered submergence tolerance. • The analysis identified 34 genes that were ubiquitously co-regulated by submergence and O(2) deprivation. The biological functions of these include signaling, transcription, and anaerobic energy metabolism. HUPs comprised 40% of the co-regulated transcripts and mutants of seven of these genes were significantly altered in submergence tolerance. • The results define transcriptomic adjustments in response to submergence in the dark and demonstrate that the manipulation of HUPs can alter submergence tolerance.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Arabidopsis / cytology
  • Arabidopsis / drug effects
  • Arabidopsis / genetics*
  • Arabidopsis / physiology*
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism
  • Carbon / metabolism
  • Cell Hypoxia / drug effects
  • Cell Hypoxia / genetics
  • Cell Proliferation / drug effects
  • Cluster Analysis
  • Darkness
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant / drug effects
  • Genes, Plant / genetics
  • Organ Specificity / drug effects
  • Organ Specificity / genetics
  • Oxygen / metabolism
  • Partial Pressure
  • Plant Roots / drug effects
  • Plant Roots / metabolism
  • Stress, Physiological / drug effects
  • Stress, Physiological / genetics
  • Time Factors
  • Transcription Factors / genetics
  • Transcription Factors / metabolism
  • Water / pharmacology*


  • Arabidopsis Proteins
  • Transcription Factors
  • Water
  • Carbon
  • Oxygen