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DEVELOPMENT AND HORMONE ACTION

Elucidating the Germination Transcriptional Program Using Small Molecules^1,[W],[OA]

Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2 (G.W.B., P.F., J.A.F., N.J.P.); Centre for the Analysis of Genome Evolution and Function, Toronto, Ontario, Canada M5S 3B2 (P.F., N.J.P.); Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada M5G 1L5 (T.-f.F.C.); and Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (S.R.C.)

The transition from seed to seedling is mediated by germination, a complex process that starts with imbibition and completes with radicle emergence. To gain insight into the transcriptional program mediating germination, previous studies have compared the transcript profiles of dry, dormant, and germinating after-ripened Arabidopsis (Arabidopsis thaliana) seeds. While informative, these approaches did not distinguish the transcriptional responses due to imbibition, shifts in metabolism, or breaking of dormancy from those triggered by the initiation of germination. In this study, three mechanistically distinct small molecules that inhibit Arabidopsis seed germination (methotrexate, 2, 4-dinitrophenol, and cycloheximide) were identified using a small-molecule screen and used to probe the germination transcriptome. Germination-responsive transcripts were defined as those with significantly altered transcript abundance across all inhibitory treatments with respect to control germinating seeds, using data from ATH1 microarrays. This analysis identified numerous germination regulators as germination responsive, including the DELLA proteins GAI, RGA, and RGL3, the abscisic acid-insensitive proteins ABI4, ABI5, ABI8, and FRY1, and the gibberellin receptor GID1A. To help visualize these and other publicly available seed microarray data, we designed a seed mRNA expression browser using the electronic Fluorescent Pictograph platform. An overall decrease in gene expression and a 5-fold greater number of transcripts identified as statistically down-regulated in drug-inhibited seeds point to a role for mRNA degradation or turnover during seed germination. The genes identified in our study as responsive to germination define potential uncharacterized regulators of this process and provide a refined transcriptional signature for germinating Arabidopsis seeds.

² These authors contributed equally to the research in this work.

³ These authors contributed equally to the supervision of this work.

The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantphysiol.org) is: Sean R. Cutler (sean.cutler{at}ucr.edu).

^[W] The online version of this article contains Web-only data.

^[OA] Open Access articles can be viewed online without a subscription.

www.plantphysiol.org/cgi/doi/10.1104/pp.107.110841

^* Corresponding author; e-mail sean.cutler{at}ucr.edu.

Received October 16, 2007; accepted March 3, 2008; published March 21, 2008.

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