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Open Access Research article

Comparing genomic expression patterns across plant species reveals highly diverged transcriptional dynamics in response to salt stress

Harkamal Walia1*, Clyde Wilson3, Abdelbagi M Ismail4, Timothy J Close2 and Xinping Cui5

Author Affiliations

1 Department of Plant Pathology, University of California, Davis, CA, USA

2 Department of Botany and Plant Sciences, University of California, Riverside, CA, USA

3 USDA-ARS, U. S. Salinity Laboratory, Riverside, CA, USA

4 Crop and Environmental Sciences Division, International Rice Research Institute, Philippines

5 Department of Statistics, University of California, Riverside, CA, USA

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BMC Genomics 2009, 10:398  doi:10.1186/1471-2164-10-398

Published: 25 August 2009



Rice and barley are both members of Poaceae (grass family) but have a marked difference in salt tolerance. The molecular mechanism underlying this difference was previously unexplored. This study employs a comparative genomics approach to identify analogous and contrasting gene expression patterns between rice and barley.


A hierarchical clustering approach identified several interesting expression trajectories among rice and barley genotypes. There were no major conserved expression patterns between the two species in response to salt stress. A wheat salt-stress dataset was queried for comparison with rice and barley. Roughly one-third of the salt-stress responses of barley were conserved with wheat while overlap between wheat and rice was minimal. These results demonstrate that, at transcriptome level, rice is strikingly different compared to the more closely related barley and wheat. This apparent lack of analogous transcriptional programs in response to salt stress is further highlighted through close examination of genes associated with root growth and development.


The analysis provides support for the hypothesis that conservation of transcriptional signatures in response to environmental cues depends on the genetic similarity among the genotypes within a species, and on the phylogenetic distance between the species.