Genomics of Stress Escape in Arabidopsis Thaliana

In nature, two highly diverse environmental signals, flooding and shade, sensed through their own unique receptor systems, share physiological and molecular similarities in the context of accelerated shoot elongation in plants (a conserved stress-escape strategy), suggesting a possible cross-talk between the two signals. This shoot elongation response is mediated by ethylene accumulating in flooding and by changes in light quality and quantity under vegetation shade. Our aim was to find out the common physiological regulators of this elongation phenotype, as it becomes easy to limit this fast growth and thereby conserve energy and increase plant yield in different stresses (similar to semi-dwarf crop varieties of green revolution with mutated GA20OX1). We adopted hypocotyl elongation as a proxy for shoot elongation and delineated Arabidopsis hypocotyl length kinetics in response to ethylene and shade. Based on the kinetics, we further investigated ethylene and shade-induced genome-wide temporal gene expression changes in hypocotyls and cotyledons separately. Hypocotyl transcriptome was reconfigured more than the cotyledon transcriptome. Bioinformatics analyses hinted towards contrasting regulation of growth promotion- and photosynthesis-related genes. Correlational analysis of organ-specific transcriptomic changes to hormone microarray data suggested a strong induction of auxin, brassinosteroid and gibberellin signatures in the elongating hypocotyls. Finally, we characterized and discussed the possible connections between the candidate genes to give an overview of the signal integration between ethylene and shade during hypocotyl growth in response to the two signals. We found evidence of both negative and positive players being transcriptionally induced by same stresses to modulate growth and by using the same set of hormone genes. In nature, plants often encounter various environmental stresses simultaneously. As such using a conserved set of molecular players to resist many stresses is advantageous to the plants.