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

Authors: WALIA, HARKAMAL - University Of California; Wilson, Clyde; ISMAIL, ABDELBAGI - International Rice Research Institute; CLOSE, TIMOTHY - University Of California; CUI, XINPING - University Of California

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/25/2009
Publication Date: 9/25/2009
Citation: Walia, H., Wilson, C., Ismail, A.M., Close, T.J., Cui, X. 2009. Comparing genomic expression patterns across plant species reveals highly diverged transcriptional dynamics in response to salt stress. Biomed Central (BMC) Genomics. 10:1471-2164.

Interpretive Summary: Crops plants growing in the field face many stresses. One stress that is a major factor in reducing crop yields is salinity stress. In order to survive and reproduce in stress environments, many plants have developed adaptive tolerance mechanisms. Recent studies in our laboratory examined the molecular mechanisms underlying the difference in salt tolerance of a major salt tolerant crop (barley) and salt-sensitive crop (rice). In this study, we looked for genes which are expressed similarly and differently between barley and rice in response to salinity stress. Our analysis did not find any major similar expression patterns between the barley and rice in response to salt stress. We then compared both barley and rice with another crop, the moderately tolerant wheat. We found that the expression pattern of several genes to be similar between barley and wheat, but not barley and rice. This work supports the idea that gene response to environmental stresses depends on having a similar genome within a species, and on the evolutionary distance between the species. These findings should aid cereal breeders in that the analysis identifies source similar and dissimilar germplasm which may used by breeders to develop salt-tolerant crops.

Technical Abstract: 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. Surprisingly, the analysis did not reveal any 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 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.