An atlas of gene expression from seed to seed through barley development

Arnis Druka, Gary Muehlbauer, Ilze Druka, Rico Caldo, Ute Baumann, Nils Rostoks, Andreas Schreiber, Roger Wise, Timothy Close, Andris Kleinhofs, Andreas Graner, Alan Schulman, Peter Langridge, Kazuhiro Sato, Patrick Hayes, Jim McNicol, David Marshall, Robbie Waugh

Research output: Contribution to journalArticle

112 Citations (Scopus)

Abstract

Assaying relative and absolute levels of gene expression in a diverse series of tissues is a central step in the process of characterizing gene function and a necessary component of almost all publications describing individual genes or gene family members. However, throughout the literature, such studies lack consistency in genotype, tissues analyzed, and growth conditions applied, and, as a result, the body of information that is currently assembled is fragmented and difficult to compare between different studies. The development of a comprehensive platform for assaying gene expression that is available to the entire research community provides a major opportunity to assess whole biological systems in a single experiment. It also integrates detailed knowledge and information on individual genes into a unified framework that provides both context and resource to explore their contributions in a broader biological system. We have established a data set that describes the expression of 21,439 barley genes in 15 tissues sampled throughout the development of the barley cv. Morex grown under highly controlled conditions. Rather than attempting to address a specific biological question, our experiment was designed to provide a reference gene expression data set for barley researchers; a gene expression atlas and a comparative data set for those investigating genes or regulatory networks in other plant species. In this paper we describe the tissues sampled and their transcriptomes, and provide summary information on genes that are either specifically expressed in certain tissues or show correlated expression patterns across all 15 tissue samples. Using specific examples and an online tutorial, we describe how the data set can be interrogated for patterns and levels of barley gene expression and how the resulting information can be used to generate and/or test specific biological hypotheses.

Original languageEnglish
Pages (from-to)202-211
Number of pages10
JournalFunctional and Integrative Genomics
Volume6
Issue number3
DOIs
Publication statusPublished - Jul 1 2006

Keywords

  • Barley
  • Development
  • Gene expression

ASJC Scopus subject areas

  • Genetics

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  • Cite this

    Druka, A., Muehlbauer, G., Druka, I., Caldo, R., Baumann, U., Rostoks, N., Schreiber, A., Wise, R., Close, T., Kleinhofs, A., Graner, A., Schulman, A., Langridge, P., Sato, K., Hayes, P., McNicol, J., Marshall, D., & Waugh, R. (2006). An atlas of gene expression from seed to seed through barley development. Functional and Integrative Genomics, 6(3), 202-211. https://doi.org/10.1007/s10142-006-0025-4