Plastic and adaptive gene expression patterns associated with temperature stress in Arabidopsis thaliana

Transcriptional profiling using DNA microarrays has become a widely used approach for identifying genes with important roles in stress-regulatory networks. In previous studies, genes exhibiting a plastic expression pattern with respect to stress and control treatments have been identified as candidates with putative roles in stress-response pathways. This approach, however, often identifies numerous genes, and it is difficult to discern which genes have major effects that impact the fitness of individuals under stress. In this study, we investigated the impacts of temperature stress (cold and heat) on gene expression in the Arabidopsis thaliana model system. We identified genes exhibiting plastic patterns of gene expression with respect to temperature stress, but in contrast to previous studies, we also considered the adaptive significance of genes by examining their expression patterns among 10 Arabidopsis ecotypes indigenous to a range of latitudes. Our findings support a general association between plasticity of gene expression and adaptive value. In comparison to non-plastic genes, genes exhibiting plastic expression patterns were associated with greater among-ecotype variation in expression levels, and such variation was more strongly correlated with geographical temperature gradients. Surprisingly, while more than 16 000 genes were associated with plastic expression patterns, significant evidence of both expression plasticity and adaptive value was obtained for only 43 genes. These selected genes represent strong candidates for future experimental investigations into the molecular basis of temperature acclimation in the A. thaliana model system.