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JXB Advance Access published online on November 17, 2008
Journal of Experimental Botany, doi:10.1093/jxb/ern270
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© 2008 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. This paper is available online free of all access charges (see http://jxb.oxfordjournals.org/open_access.html for further details)

RESEARCH PAPER

A pathway-specific microarray analysis highlights the complex and co-ordinated transcriptional networks of the developing grain of field-grown barley

Michael Hansen1, Carsten Friis2, Steve Bowra3, Preben Bach Holm1 and Eva Vincze1,*

1Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Research Centre Flakkebjerg, DK-4200 Slagelse, Denmark
2Center for Biological Sequence Analysis, BioCentrum, Technical University of Denmark, Building 208, DK-2800, Lyngby, Denmark
3Verzyme (UK) Ltd., Plas Gogerddan, Aberystwyth, Wales SY23 3EB, UK

* To whom correspondence should be addressed: E-mail: eva.vincze{at}agrsci.dk

The aim of the study was to describe the molecular and biochemical interactions associated with amino acid biosynthesis and storage protein accumulation in the developing grains of field-grown barley. Our strategy was to analyse the transcription of genes associated with the biosynthesis of storage products during the development of field-grown barley grains using a grain-specific microarray assembled in our laboratory. To identify co-regulated genes, a distance matrix was constructed which enabled the identification of three clusters corresponding to early, middle, and late grain development. The gene expression pattern associated with the clusters was investigated using pathway-specific analysis with specific reference to the temporal expression levels of a range of genes involved mainly in the photosynthesis process, amino acid and storage protein metabolism. It is concluded that the grain-specific microarray is a reliable and cost-effective tool for monitoring temporal changes in the transcriptome of the major metabolic pathways in the barley grain. Moreover, it was sensitive enough to monitor differences in the gene expression profiles of different homologues from the storage protein families. The study described here should provide a strong complement to existing knowledge assisting further understanding of grain development and thereby provide a foundation for plant breeding towards storage proteins with improved nutritional quality.

Key words: Amino acid metabolism, cDNA microarray, field trial, hordein, Hordeum vulgare, storage proteins

Received 30 July 2008; Revised 8 October 2008 Accepted 9 October 2008


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