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Open Access Highly Accessed Open Badges Research article

Connecting genes, coexpression modules, and molecular signatures to environmental stress phenotypes in plants

David J Weston1*, Lee E Gunter1, Alistair Rogers23 and Stan D Wullschleger1

Author Affiliations

1 Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6422, USA

2 Environmental Sciences Department, Brookhaven National Laboratory, Upton, NY 11973-5000, USA

3 Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA

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BMC Systems Biology 2008, 2:16  doi:10.1186/1752-0509-2-16

Published: 4 February 2008



One of the eminent opportunities afforded by modern genomic technologies is the potential to provide a mechanistic understanding of the processes by which genetic change translates to phenotypic variation and the resultant appearance of distinct physiological traits. Indeed much progress has been made in this area, particularly in biomedicine where functional genomic information can be used to determine the physiological state (e.g., diagnosis) and predict phenotypic outcome (e.g., patient survival). Ecology currently lacks an analogous approach where genomic information can be used to diagnose the presence of a given physiological state (e.g., stress response) and then predict likely phenotypic outcomes (e.g., stress duration and tolerance, fitness).


Here, we demonstrate that a compendium of genomic signatures can be used to classify the plant abiotic stress phenotype in Arabidopsis according to the architecture of the transcriptome, and then be linked with gene coexpression network analysis to determine the underlying genes governing the phenotypic response. Using this approach, we confirm the existence of known stress responsive pathways and marker genes, report a common abiotic stress responsive transcriptome and relate phenotypic classification to stress duration.


Linking genomic signatures to gene coexpression analysis provides a unique method of relating an observed plant phenotype to changes in gene expression that underlie that phenotype. Such information is critical to current and future investigations in plant biology and, in particular, to evolutionary ecology, where a mechanistic understanding of adaptive physiological responses to abiotic stress can provide researchers with a tool of great predictive value in understanding species and population level adaptation to climate change.