Molecular characterization of the submergence response of the Arabidopsis thaliana ecotype Columbia
Article first published online: 13 JAN 2011
© 2011 The Authors. New Phytologist © 2011 New Phytologist Trust
Special Issue: Plant anaerobiosis
Volume 190, Issue 2, pages 457–471, April 2011
How to Cite
Lee, S. C., Mustroph, A., Sasidharan, R., Vashisht, D., Pedersen, O., Oosumi, T., Voesenek, L. A.C.J. and Bailey-Serres, J. (2011), Molecular characterization of the submergence response of the Arabidopsis thaliana ecotype Columbia. New Phytologist, 190: 457–471. doi: 10.1111/j.1469-8137.2010.03590.x
- Issue published online: 28 MAR 2011
- Article first published online: 13 JAN 2011
- Received: 19 September 2010, Accepted: 8 November 2010
- anaerobic metabolism;
- oxygen content;
- oxygen deprivation;
- unknown protein
- •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 O2 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 O2-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 O2 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.