Plant Molecular Biology 52: 873–891, 2003. © 2003 Kluwer Academic Publishers. Printed in the Netherlands. 873 Temporal progression of gene expression responses to salt shock in maize roots Hong Wang 1 , Saori Miyazaki 2,5 , Kiyoshi Kawai 2 , Michael Deyholos 1,4 , David W. Galbraith 1 and Hans J. Bohnert 1,2,3,5,∗ 1 Department of Plant Sciences, 2 Department of Biochemistry and Molecular Biophysics, and 3 Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA; 4 Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada; 5 Department of Plant Biology and Depart- ment of Crop Sciences, University of Illinois, 1201 W. Gregory Drive, Urbana, IL 61801, USA ( ∗ author for correspondence; e-mail bohnerth@life.uiuc.edu) Received 27 December 2002; accepted in revised form 8 April 2003 Key words: gene expression profile, microarray, salt stress, time course, Zea mays Abstract Using a cDNA microarray containing 7943 ESTs, the behavior of the maize root transcriptome has been monitored in a time course for 72 h after imposition of salinity stress (150 mM NaCl). Under these conditions, root sodium amounts increased faster than in leaves, and root potassium decreased significantly. Although the overall free amino acid concentration was not affected, amino acid composition was changed with proline and asparagine increasing. Microarray analysis identified 916 ESTs representing genes whose steady-state RNA levels were significantly altered at various time points, corresponding to 11% of the ESTs printed. The response of the transcriptome to sub-lethal salt stress was rapid and transient, leading to a burst of changes at the three-hour time point. The salt- regulated ESTs represented 472 tentatively unique genes (TUGs), which, based on functional category analysis, are involved in a broad range of cellular and biochemical activities, prominent amongst which were transport and signal transduction pathways. Clustering of regulated transcripts based on the timing and duration of changes suggests a structured succession of induction and repression for salt responsive genes in multiple signal and response cascades. Within this framework, 16 signaling molecules, including six protein kinases, two protein phosphatases and eight transcription factors, were regulated with distinct expression patterns by high salinity. Introduction High soil salinity constitutes abiotic stress, which can impair plant growth and development and limit agri- cultural productivity. Worldwide, about one fifth of all cultivated land and nearly half the irrigated area are affected by salinity (Rhoades and Loveday, 1990). Under conditions of high salinity, plants experience two kinds of stresses: ionic, in which high amounts primarily of sodium in the soil disrupt cellular ion homeostasis, and osmotic, in which increased amounts of sodium reduce water availability by decreasing the osmotic potential of the soil. High salinity also el- evates oxidative stress, as plants attempt to regain homeostasis and redox control, repair damage, and adjust metabolism (Asada, 1994; Noctor and Foyer, 1998; Halliwell and Gutteridge, 1999). In order to adapt to, and then survive in, highly saline environments, plants must modulate biochem- ical activities and development based on stress sens- ing and salt stress-responsive signal transduction (Hasegawa et al., 2000; Shinozaki and Yamaguchi- Shinozaki, 2000; Zhu, 2001; Zhu, 2002). Among the most prevalent adaptive responses are attempts to achieve ion and water homeostasis, to attain os- motic adjustment, and to enhance protective measures that reduce oxidative damage. Different species have evolved alternative pathways for protection, such as those leading to either Na + exclusion or vacuolar com-