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Published on March 21, 2008; 10.1104/pp.107.110841

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Received October 16, 2007
Accepted March 3, 2008

Elucidating the germination transcriptional program using small molecules

George W. Bassel , Pauline Fung , Tsz-fung Freeman Chow , Justin A. Foong , Nicholas J. Provart , and Sean R. Cutler *

Department of Cell and Systems Biology, University of Toronto, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada; Centre for the Analysis of Genome Evolution and Function, 25 Willcocks St., Toronto, ON, M5S 3B2, Canada; Current address, Department of Laboratory Medicine and Pathobiology, University of Toronto, 100 College Street, Room 110, Toronto, ON, M5G 1L5, CANADA; Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California-Riverside, 5451 Boyce Hall, Riverside, CA, 92521, USA

* Corresponding author; email: sean.cutler{at}ucr.edu.

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 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 ABA-Insensitive proteins ABI4, ABI5, ABI8, FRY1 and the GA receptor GID1A. To help visualize these, and other publicly available seed microarray data, we designed a seed mRNA expression browser using the eFP platform. An overall decrease in gene expression and a five-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.






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