Abstract
Plant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley (Hordeum vulgare) grain maturation, desiccation, and germination in two tissue fractions (starchy endosperm/aleurone and embryo/scutellum) using the Affymetrix Barley1 GeneChip. To aid data evaluation, Arabidopsis thaliana MapMan and PageMan tools were adapted to barley. The analyses allow a number of conclusions: (1) Cluster analysis revealed a smooth transition in transcription programs between late seed maturation and germination within embryo tissues, but not in the endosperm/aleurone. (2) More than 12,000 transcripts are stored in the embryo of dry barley grains, many of which are presumably activated during germination. (3) Transcriptional activation of storage reserve mobilization events occurs at an early stage of germination, well before radicle protrusion. (4) Key genes of gibberellin (GA) biosynthesis are already active during grain maturation at a time when abscisic acid peaks suggesting the formation of an endogenous store of GA in the aleurone. This GA probably acts later during germination in addition to newly synthesized GA. (5) Beside the well-known role of GA in gene activation during germination spatiotemporal expression data and cis-element searches in homologous rice promoters confirm an equally important gene-activating role of abscisic acid during this developmental period. The respective regulatory webs are linked to auxin and ethylene controlled networks. In summary, new bioinformatics PageMan and MapMan tools developed in barley have been successfully used to investigate in detail the transcriptome relationships between seed maturation and germination in an important crop plant.
Highlights
Plant seeds prepare for germination already during seed maturation
In this study we extend our investigation on barley grain development (Sreenivasulu et al, 2006) by a combined analysis of grain maturation, desiccation, and germination
We used the Affymetrix Barley1 GeneChip for transcriptome analysis in contrast to the 12K macro array of earlier work with genes only expressed during grain development
Summary
Plant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley (Hordeum vulgare) grain maturation, desiccation, and germination in two tissue fractions (starchy endosperm/aleurone and embryo/scutellum) using the Affymetrix Barley GeneChip. The two processes were analyzed separately and, these studies do not reflect the detailed links between grain maturation and germination at the transcriptome level To close this gap we analyzed barley grain batches with the help of the Affymetrix Barley GeneChip (Close et al, 2004) at several time points during both grain maturation and germination with the following aims: (1) to catalog gene expression patterns during grain development across the dormant quiescence period; (2) to analyze the expression patterns by new bioinformatics tools adapted for barley to define groups of carefully annotated, coregulated genes that are specific for two hand-prepared tissue fractions, starchy endosperm/aleurone and embryo/scutellum; (3) to infer interaction networks by postulating DNAprotein interactions based on defined cis-elements in orthologous rice (Oryza sativa) gene upstream regions; and (4) to extend our knowledge on hormonal regulation and interaction during seed development and germination by analyzing the temporal and spatial changes in expression of hormone biosynthetic and deactivating genes in the two analyzed tissue fractions. Further hints for the deduced regulatory networks come from specific cis-elements found in the 5#-upstream regions of homologous rice genes
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