Seed germination is a complex, multistage process that can be divided into three phases of imbibition, increased metabolic activity and initiation of growth, which loosely parallel the triphasic water uptake of dry mature seeds. Morphologically, initiation of growth corresponds to radicle emergence, and subsequent growth is generally defined as seedling growth. By definition, germination sensu stricto incorporates those events that start with the uptake of water by the non-dormant quiescent dry seed and terminate with the protrusion of the radicle and the elongation of the embryonic axis (Bewley and Black, 1994). Upon imbibition, the quiescent dry seed rapidly resumes metabolic activity. To explore genome-wide expression patterns of this complex developmental process, parallel protein and mRNA profiling studies of dry and imbibed seeds have been conducted, during the last few years, using the model plant Arabidopsis (Arabidopsis thaliana (L.) Heynh.). The widespread acceptance of Arabidopsis as a model plant is based on the genetic and genomic methods and resources that are available for it, which have facilitated the investigation of a range of biological problems (see Somerville and Koornneef, 2002 for a review). Our results show that new insights into this complex developmental pathway can be extracted from such global expression-profiling approaches.

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