We analysed the transcriptome of the two major parts of barley seeds, embryo and endosperm, throughout development using a 12 k cDNA array of seed-expressed unigenes. We focussed on transcriptional regulators/transcription factors (TFs), kinases and signalling networks. Correlation analysis of gene expression patterns demonstrated interactions of transcriptional and hormonal regulators during grain maturation. We propose that ABA in the starchy endosperm is controlling starch synthesis via SNF1 kinase, whereas ABAresponsive genes active during embryo maturation are involved in the control of lipid storage. Via ABA responsive element binding factors, ABA is furthermore believed to control acquisition of desiccation tolerance but the data also suggest an ABA independent but interactive pathway via DREB transcription factors. In an attempt to gain insight into the underlying genetic factors that govern differences in storage product accumulation we compared changes in gene expression during seed development among 42 homozygous lines carrying defined segments of a wild barley (Hordeum spontaneum) genome introgressed into the elite H. vulgare cv. 'Brenda' background and dissected the candidate regulatory genes involved in altering storage products.