Polyploidy has long been recognized as a prominent force shaping the evolution of flowering plants. However, the causes of novel variation in polyploids are not well understood. Therefore, a comprehensive survey of global gene expression in response to polyploidy was performed by using an Arabidopsis thaliana whole genome Affymetrix gene chip (ATH1) to quantify the variations in transcript abundance of 22,810 genes between autotetraploid and diploid Isatis indigotica Fort., which is the same family, Cruciferae, as Arabidopsis thaliana. The analysis revealed a coordinated induction and suppression of 715 and 251 ploidy-responsive genes in autotetraploid Isatis indigotica Fort., respectively. The functional classification of some of these up-regulated genes indicates their involvement in various metabolic, signal transduction, transcriptional regulation, and developmental pathways. The results enhance our knowledge about molecular processes associated with autopolyploidy.
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