Comparative transcriptome analysis of responses of Arabidopsis ecotypes to cold stress

Transcriptional variation, also called expression level polymorphism (ELP), contributes to intra-specific phenotypic variation in many organisms. Differentially expressed transcripts are typically enriched for stress-related genes, suggesting that differences in response to the environment are a particularly common point of divergence among gentoypes. Analysis of ELPs also has been suggested as a way to assess unintended consequences of transgene introduction; however, it is important that interpretation of transcriptional changes be performed within the context of potential fitness effects. In these studies we sought to examine differential gene expression in response to cold for two widely used Arabidopsis thaliana ecotypes, C24 and Columbia (Col). Two Arabidopsis genotypes were grown in 1/2 MS plate. Forteen-day-old seedlings were used for RNA extraction and hybridization on Affymetrix microarrays. There were two biological replicates for each genotype and cold treatment combination.