Using Specialized cDNA Microarrays to Analyze Arabidopsis Gene Expression Under Cold Stress

Abstract

Cold acclimation enables plants to withstand low but non-freezing temperatures. Biochemical and physiological changes include a reduction in tissue water content and altered composition of membrane lipids. These responses are correlated with fluctuations in the expression of cold-induced genes such as LTI (low-temperature-induced), KIN (cold-inducible), RD (responsive to desiccation), and ERD (early dehydration-inducible). We performed time-course experiments with specialized cDNA microarrays comprising 712 cDNAs selected by SAGE and SSH methods. Expression dynamics were monitored in the leaves of Arabidopsis. Profiles of nine samples from plants chilled for various time periods revealed 264 cold-inducible genes and 33 repressed genes, for which expression was altered (up or down) by at least twofold. These included not only several previously reported cold-regulated genes, e.g., rd, lea, and CBF3, but also candidate genes such as those for alcohol dehydrogenase and transport inhibitor response 1. All genes were grouped according to their expression patterns; most tended to shift their expression at 3 ∼ 8 h after cold treatment. Two cold-associated transcriptional activators, CBF2 and CBF3, did not have parallel patterns of expression, although both were induced within 15 min. Our results suggest different roles for CBF2 and CBF3 in the signal-transduction pathway for cold acclimation. We believe that, compared with standard differential screening, our microarray analysis is a more useful technique for the selection of new candidate genes responsible for cold acclimation.