Phenotypic divergence can often be traced to gene expression variation. Gene expression variation resulting in phenotypic differences has been observed among individuals within a population, a species and across multiple species [1
]. Although instances of phenotypic divergence and underlying expression variation were reported in the past, it was the advent of reliable microarray technology that enabled biologists to study expression variation at a whole-genome level and link it to phenotypic variation.
Several studies have focused on expression level variation among accession within the species and between species in Drosophila
, primates, yeast and fish [1
]. In the plant kingdom, however, comparative genomics expression analyses across species have been scarce. One noteworthy comparative interspecies experiment sampled different tissues and revealed a low correlation for conserved expression pattern between rice and Arabidopsis
]. The comparison between these highly diverged model species representing the monocots and dicots was elaborated upon by measuring their responses to light and dark regimes in two tissue types [7
]. The comparisons indicated expression level conservation to some degree during the light regime but not in changes triggered in response to darkness. The study further indicated a lack of conservation in response to light between shoot and root tissue, thus highlighting the significance of tissue level variation that exist in inter- and intra-species comparisons [8
]. A comparison between two ecotypes of A
at early seedling stage identified about 8% of the transcriptome to be differentially expressed. Notably, genes with a difference in transcript abundance were enriched in genes responsive to environmental factors [9
Studies comparing the transcriptomes of multiple species have provided insights on phenotypic variation and accompanying expression variation. However, the biological interpretation can be challenging due to large and diverse sets of genes which are expressed differently across species. A more targeted approach for multi-species comparative expression analysis is to determine how different species respond to a particular perturbation such as starvation, exposure to chemicals or a naturally occurring environmental stress. For instance in plants, the transcriptome of Arabidopsis thaliana
and a salt-tolerant Thellungiella halophila
have been compared for their response to salt stress [10
]. An important finding of these studies was that the highly tolerant Thellungiella halophila
had several salt-tolerance related genes constitutively expressed at a higher level compared to A. thaliana
even in absence of stress. In the present study, the focus was on the differential response patterns of two distantly related plant species to salt stress. Two economically important members from the Poaceae
, rice and barley, were selected and profiled with respect to the deviation in their transcriptional signatures upon exposure to salt stress.
Rice is highly susceptible to even moderate levels of salinity. In contrast, barley is among the most salt-tolerant cereal crops. Physiological approaches have been employed previously to characterize the phenotypic variation in salt tolerance for these two grass species [12
]. The transcriptional responses of rice and barley genotypes were also characterized independently by several laboratories using various microarray platforms [13
]. However, a detailed comparative genomics approach to elucidate how and why these species differ in their tolerance to salt stress at molecular level remains to be pursued.
Although a comparison between rice and barley at the expression level can be performed in silico using existing datasets, such an approach has some limitations. For instance, most of the experiments involve varying levels and durations of stress imposed on plants. Further, the developmental stage at which stress is imposed varies widely. These issues are expected to inflate the observed expression level variations. Since most of the previous studies only employ a single genotype of rice or barley for expression analysis, the generality of the interpretations is limited. In this study we have used an equivalent stress level, a cognate developmental stage, similar tissue, identical microarray technology and an identical statistical analysis to compare the expression differences between rice and barley as well as within the genera.
The basic research questions which we sought to address in the present study are as follows: How conserved or different are the responses of rice and barley genes upon exposure to salt stress? Is there any species specific activation or repression of pathway(s) which can be associated with salt-tolerance of barley or sensitivity of rice?