Functional & Integrative Genomics

, Volume 6, Issue 3, pp 202–211

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
Original Paper

DOI: 10.1007/s10142-006-0025-4

Cite this article as:
Druka, A., Muehlbauer, G., Druka, I. et al. Funct Integr Genomics (2006) 6: 202. doi:10.1007/s10142-006-0025-4

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.

Keywords

BarleyDevelopmentGene expression

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Arnis Druka
    • 1
  • Gary Muehlbauer
    • 2
  • Ilze Druka
    • 1
  • Rico Caldo
    • 3
    • 4
  • Ute Baumann
    • 5
  • Nils Rostoks
    • 1
  • Andreas Schreiber
    • 5
  • Roger Wise
    • 3
    • 4
    • 6
  • Timothy Close
    • 7
  • Andris Kleinhofs
    • 8
    • 9
  • Andreas Graner
    • 10
  • Alan Schulman
    • 11
    • 12
  • Peter Langridge
    • 5
  • Kazuhiro Sato
    • 13
  • Patrick Hayes
    • 14
  • Jim McNicol
    • 15
  • David Marshall
    • 1
  • Robbie Waugh
    • 1
  1. 1.Scottish Crop Research InstituteScotlandUK
  2. 2.Department of Agronomy and Plant GeneticsUniversity of MinnesotaSt PaulUSA
  3. 3.Department of Plant PathologyIowa State UniversityAmesUSA
  4. 4.Center for Plant Responses to Environmental StressesIowa State UniversityAmesUSA
  5. 5.University of Adelaide, Plant ScienceGlen OsmondAustralia
  6. 6.Corn Insects and Crop Genetics Research, USDA-ARSIowa State UniversityAmesUSA
  7. 7.Department of Botany and Plant SciencesUniversity of CaliforniaRiversideUSA
  8. 8.Department of Crop and Soil SciencesWashington State UniversityPullmanUSA
  9. 9.Department of Genetics and Cell BiologyWashington State UniversityPullmanUSA
  10. 10.Institut für Pflanzengenetik und KulturpflanzenforschungGaterslebenGermany
  11. 11.MTT/BI Plant Genomics LaboratoryUniversity of HelsinkiHelsinkiFinland
  12. 12.MTT Agrifood Research FinlandHelsinkiFinland
  13. 13.Research Institute for BioresourcesOkayama UniversityKurashikiJapan
  14. 14.Department of Crop and Soil ScienceOregon State UniversityCorvallisUSA
  15. 15.BioSS Office, Scottish Crop Research InstituteScotlandUK