Global analysis of gene expression in maize leaves treated with low temperature. I. Moderate chilling (14 °C)

Maize yield is limited by its cold-sensitivity, the molecular mechanisms of which are poorly understood. We investigated transcriptome changes in maize leaves subjected to 14 °C for 4 (alarm phase) or 28 (acclimation phase) hours using Maize Oligonucleotide Array Project chips containing ca. 57,000 probes. To facilitate global analyses, we assigned Gene Ontology annotations to 10,171 probes using rice and Arabidopsis proteomes as basis. Additionally, gene-by-gene analysis of differentially expressed genes was done basing on annotations provided by microarray producer to indicate those most promising for further studies. Microarray results were validated by qRT-PCR. Chilling affected 440 (4 h) or 155 (28 h) transcripts. After 4 h, 59 transcripts showed aberrant response to photoperiod, suggesting diurnal clock disruption as a mechanism by which chilling affects maize physiology. GO-based analysis indicated modification of cell wall properties as another early response. Few photosynthesis-related genes were repressed by chilling, despite the popular notion that photosynthetic apparatus is a major target of cold. Conversely, induction of chloroplast-related genes not directly engaged in photosynthesis was evident at later stages of the response. Numerous transcripts strongly affected by chilling were of unknown function; they may encode novel activities crucial in maize response to chilling and deserve detailed studies.