Genome-wide in silico identification and experimental confirmation of abscisic acid-regulated genes in Arabidopsis

The abscisic acid (ABA) hormone plays a major role in various aspects of plant growth and development, including seed maturation and germination, as well as adaptation to abiotic environmental stresses. With the purpose to identify novel ABA-regulated genes, we tried to genome-wide identification of ABA-related genes using computational approach by searching ABA-responsive elements (ABREs, T/CACGTGT/GC) in entire Arabidopsis genome. 137 ABA-regulated candidate genes were found to possess two or more ABREs in the 1200-bp upstream region of the translation start site. In an attempt to monitor the gene expression of these candidates in response to ABA, 16 genes were selected and examined by RT-PCR. Of these 16, seven are unclassified genes in Arabidopsis, 12 candidates were up-regulated by ABA and four had equal expression levels as control. In addition, Northern blot analysis indicated that some candidates were further shown to differentially respond to various stresses. The results suggested that these ABA-regulated genes may consist of other cis-acting elements responsive to abiotic stresses and confirmed that in silico cloning of ABA-regulated genes through Arabidopsis genomic sequence database mining is a fast and reliable approach.