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Molecular characterization of the submergence response of the Arabidopsis thaliana ecotype Columbia
Author(s) -
Lee Seung Cho,
Mustroph Angelika,
Sasidharan Rashmi,
Vashisht Divya,
Pedersen Ole,
Oosumi Teruko,
Voesenek Laurentius A.C.J.,
BaileySerres Julia
Publication year - 2011
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/j.1469-8137.2010.03590.x
Subject(s) - biology , transcriptome , ecotype , arabidopsis thaliana , arabidopsis , darkness , gene , petiole (insect anatomy) , botany , microbiology and biotechnology , mutant , organogenesis , genetics , gene expression , hymenoptera
Summary• 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 HUP s can alter submergence tolerance.