Original Paper

Functional & Integrative Genomics

, Volume 6, Issue 3, pp 202-211

First online:

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

  • Arnis DrukaAffiliated withScottish Crop Research Institute
  • , Gary MuehlbauerAffiliated withDepartment of Agronomy and Plant Genetics, University of Minnesota
  • , Ilze DrukaAffiliated withScottish Crop Research Institute
  • , Rico CaldoAffiliated withDepartment of Plant Pathology, Iowa State UniversityCenter for Plant Responses to Environmental Stresses, Iowa State University
  • , Ute BaumannAffiliated withUniversity of Adelaide, Plant Science
  • , Nils RostoksAffiliated withScottish Crop Research Institute
  • , Andreas SchreiberAffiliated withUniversity of Adelaide, Plant Science
  • , Roger WiseAffiliated withDepartment of Plant Pathology, Iowa State UniversityCenter for Plant Responses to Environmental Stresses, Iowa State UniversityCorn Insects and Crop Genetics Research, USDA-ARS, Iowa State University
  • , Timothy CloseAffiliated withDepartment of Botany and Plant Sciences, University of California
    • , Andris KleinhofsAffiliated withDepartment of Crop and Soil Sciences, Washington State UniversityDepartment of Genetics and Cell Biology, Washington State University
    • , Andreas GranerAffiliated withInstitut für Pflanzengenetik und Kulturpflanzenforschung
    • , Alan SchulmanAffiliated withMTT/BI Plant Genomics Laboratory, University of HelsinkiMTT Agrifood Research Finland
    • , Peter LangridgeAffiliated withUniversity of Adelaide, Plant Science
    • , Kazuhiro SatoAffiliated withResearch Institute for Bioresources, Okayama University
    • , Patrick HayesAffiliated withDepartment of Crop and Soil Science, Oregon State University
    • , Jim McNicolAffiliated withBioSS Office, Scottish Crop Research Institute
    • , David MarshallAffiliated withScottish Crop Research Institute
    • , Robbie WaughAffiliated withScottish Crop Research Institute Email author 

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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.


Barley Development Gene expression