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

Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, University of Aarhus, Research Centre Flakkebjerg, DK-4200 Slagelse, Denmark.
Journal of Experimental Botany (Impact Factor: 5.79). 12/2008; 60(1):153-67. DOI: 10.1093/jxb/ern270
Source: PubMed

ABSTRACT 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.

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Available from: Carsten Friis, Aug 20, 2015
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    • "We have used similar approaches to study gene expression and regulation during seed development in other crop species, flax and canola (Venglat et al., 2011, 2013) (Fig. 1). Global gene expression studies of either whole seeds or different seed components have also been documented for legumes such as Medicago , soybean and scarlet runner bean (Le et al., 2007), canola (Huang et al., 2009) and monocot crop species such as rice (Xue et al., 2012), wheat (Gillies et al., 2012), maize (Sekhon et al., 2013, 2011) and barley (Hansen et al., 2009). This in-depth view of the gene expression patterns during seed development in diverse crop species has been possible because of the rapid advances made in whole genome sequencing and the development and application of a wide range of genomics tools (Edwards et al., 2013; Flavell, 2010; Morrell et al., 2012). "
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    • "Spatial and temporal transcriptome profiles represent snapshot of gene activity and thus have been extensively used for deciphering the role of individual genes/pathways or regulatory networks and plausible interactions among them (Adams 2008). In fact, in the past decade, multitude of microarray-based studies have been performed towards elucidating reproductive organ development in Arabidopsis (Alves-Ferreira et al. 2007; Becerra et al. 2006; Fait et al. 2006; Hennig et al. 2004; Wellmer et al. 2006; Wellmer et al. 2004; Zhang et al. 2005; Wilson et al. 2005b; Day et al. 2008), rice (Endo et al. 2004; Furutani et al. 2006; Hobo et al. 2008; Kondou et al. 2006; Lan et al. 2004; Hirano et al. 2008; Suwabe et al. 2008; Jiao et al. 2009; Wang et al. 2010; Fujita et al. 2010; Li et al. 2007a, b; Wang et al. 2005; Deveshwar et al. 2011), maize (Grimanelli et al. 2005; Liu et al. 2008; Lee et al. 2002), wheat (Wilson et al. 2005a), and other non-model plant systems (Hansen et al. 2009; Laitinen et al. 2005; Endo et al. 2002; Tebbji et al. 2010). One of the limitations of these studies is that most of these scored the number of probe sets rather than unique transcripts as an estimate of gene expression. "
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