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First published online February 23, 2007; 10.1104/pp.107.096057 Plant Physiology 143:1669-1679 (2007) © 2007 American Society of Plant Biologists OPEN ACCESS ARTICLE
Gene Expression Profiling Reveals Defined Functions of the ATP-Binding Cassette Transporter COMATOSE Late in Phase II of Germination1,[W],[OA]Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias, Valencia, Spain (E.C.); Crop Performance and Improvement Division, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom (E.C., S.F., F.L.T.); Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907–2010 (W.P.); and Department of Agricultural and Environmental Sciences, School of BioSciences, University of Nottingham, Nottingham LE12 5RD, United Kingdom (T.H., A.M., H.S., M.J.H.)
Phase II of germination represents a key developmental stage of plant growth during which imbibed seeds either enter stage III of germination, completing the germination process via radicle protrusion, or remain dormant. In this study, we analyzed the influence of the peroxisomal ATP-binding cassette transporter COMATOSE (CTS) on the postimbibition seed transcriptome of Arabidopsis (Arabidopsis thaliana) and also investigated interactions between gibberellin (GA) and CTS function. A novel method for analysis of transcriptome datasets allowed visualization of developmental signatures of seeds, showing that cts-1 retains the capacity to after ripen, indicating a germination block late in phase II. Expression of the key GA biosynthetic genes GA3ox1 and 2 was greatly reduced in cts seeds and genetic analysis suggested that CTS was epistatic to RGL2, a germination-repressing DELLA protein that is degraded by GA. Comparative analysis of seed transcriptome datasets indicated that specific cohorts of genes were influenced by GA and CTS. CTS function was required for expression of the flavonoid biosynthetic pathway. Confocal imaging demonstrated the exclusive accumulation of flavonoids in the epidermis of wild-type seeds. In contrast, flavonoids were absent from cts and kat2-1 mutant seeds, but accumulated following the application of sucrose, indicating an essential role for
1 This work was supported by the Exploiting Genomics Initiative, Biotechnology and Biological Research Council (BBSRC; grant to E.C.), by a Lawes Trust Ph.D. studentship (to T.H.), and by the University of Nottingham (grant to A.M. and H.S.). Rothamsted Research receives grant-aided support from the BBSRC (UK). W.P. acknowledges a National Science Foundation grant to Angus S. Murphy and an Underwood/BBSRC grant. 2 These authors contributed equally to the paper. 3 Present address: Saaten-Union Resistenzlabor GmbH, 06466 Gatersleben, Germany. 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: Michael J. Holdsworth (michael.holdsworth{at}nottingham.ac.uk). [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.107.096057 * Corresponding author; e-mail michael.holdsworth{at}nottingham.ac.uk; fax 44–1159516233. Received January 18, 2007; accepted February 13, 2007; published February 23, 2007. This article has been cited by other articles:
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-oxidation in inducing flavonoid biosynthetic genes. These results demonstrate that CTS functions very late in phase II of germination and that its function is required for the expression of specific gene sets related to an important biochemical pathway associated with seedling establishment and survival. 
