Molecular Breeding

, Volume 21, Issue 2, pp 261–269 | Cite as

Transcriptome profile of barley aleurone differs between total and polysomal RNAs: implications for proteome modeling

  • Ronald W. Skadsen
  • Peicheng Jing


Microarray analysis of mRNA populations is routinely conducted with total RNA. However, such analyses would probably represent the translated genome (proteome) more accurately if conducted with polysomal RNA. An accurate assessment of the proteome is essential where microarray analysis is used to produce molecular markers for breeding programs. In order to determine whether significant variation occurs between these two RNA populations, the relative abundance of transcripts was analyzed in barley aleurones of intact 3.5 day old germinated seedlings, comparing total and polysomal RNAs. A total of 13,744 transcripts was detected among both populations. Of these, 714 were detected only in total RNA, and 1,541 were detected only in polysomal RNA. A surprising number of transcripts detected in both populations (6,312 gene calls or 46% of the compared transcripts) differed significantly between populations. Almost half of these (2,987) were more abundant by at least two-fold, depending on the RNA source, and expression was often biased toward specific functional classes of genes. Transcripts encoding hydrolytic enzymes for the mobilization of stored seed macromolecules were more highly represented in total RNA, rather than polysomal RNA. These included proteinases, nucleases and carbohydrases. Genes for ribonucleoprotein complexes, nucleic acid binding and components of ribosomes were more abundant in polysomal RNA. Among genes with signal intensities of 1,000 or more, hydrolases were greatly over-represented in total RNA, whereas ubiquitin, histone and kinase related genes were mainly represented in polysomal RNA.


Aleurone Barley seed Microarray Polysomal mRNA Transcriptional profiling Proteome 



The pM/C clone was generously provided by John Rogers (Washington State Univ.). The 18S barley rRNA was cloned in our lab by John Herbst. This material is based upon work supported by the U.S. Department of Agriculture. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Dept. of Agriculture.


  1. Bamforth CW, Barclay AHP (1993) Malting technology and the uses of malt. In: MacGregor AW, Bhatty RS (eds) Barley: chemistry and technology. American Assoc. of Cereal Chemists, Inc., St. Paul, MNGoogle Scholar
  2. Bérengè P-B, Boulmé F, Beug H, Müllner EW, Garcia-Sanz JA (2001) Translational control: bridging the gap between genomics and proteomics? Trends Biochem Sci 26:225–229CrossRefGoogle Scholar
  3. Berger SL, Birkenmeier CS (1979) Inhibition of intractable nucleases with ribonucleoside-vanadyl complexes: isolation of messenger ribonucleic acid from resting lymphocytes. Biochemistry 18:5143–5149PubMedCrossRefGoogle Scholar
  4. Bethke PC, Hwang Y-S, Zhu T, Jones RL (2005) Global patterns of gene expression in the aleurone of wild-type and dwarf1 mutant rice. Plant Physiol 140:484–498PubMedCrossRefGoogle Scholar
  5. Boddu J, Cho S, Kruger WM, Muehlbauer GJ (2006) Transcriptome analysis of the barley-Fusarium graminearum interaction. Mol Plant Microbe Int 19:407–417CrossRefGoogle Scholar
  6. Briggs DE (1978) Barley. Chapman and Hall, London, pp 208–215Google Scholar
  7. Caldo RA, Nettleton D, Wise RP (2004) Interaction-dependent gene expression in Mla-specified response to barley powdery mildew. Plant Cell 16:2514–2528PubMedCrossRefGoogle Scholar
  8. Carrari F, Baxter C, Usadel B, Urbanczyk-Wochniac E, Zanor AN, Nikiforova V, Centero D, Ratzka A, Pauly M et al (2006) Integrated analysis of metabolite and transcript levels reveals the metabolic shifts that underlie tomato fruit development and highlight regulatory aspects of metabolic network behavior. Plant Physiol 142:1380–1396PubMedCrossRefGoogle Scholar
  9. Chandler PM, Jacobsen JV (1991) Primer extension studies on α-amylase mRNAs in barley aleurone. II. Hormonal regulation of expression. Plant Mol Biol 16:637–645PubMedCrossRefGoogle Scholar
  10. Chen K, An Y-QC (2006) Transcriptional responses to gibberellin and abscisic acid in barley aleurone. J Integr Plant Biol 48:591–612CrossRefGoogle Scholar
  11. Close TJ, Wanamaker SL, Caldo RA, Turner SM, Ashlock DA, Dickerson JA, Wing RA, Muehlbauer GJ, Kleinhofs A, Wise RP (2004) A new resource for cereal genomics: 22K barley gene chip comes of age. Plant Physiol 134:960–968PubMedCrossRefGoogle Scholar
  12. Gygi SP, Rochon Y, Franza BR, Aebersold R (1999) Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19:1720–1730PubMedGoogle Scholar
  13. Hayes PM, Castro A, Marquez-Cedillo, Corey A, Henson C, Jones B, Kling J, Mather D, Matus I, Rossi C, Sato K (2003) Genetic diversity for quantitatively inherited agronomic and malting quality traits. In: Roland von Bothmer et al. (eds) Diversity in barley (Hordeum vulgare). Elsevier Science B.VGoogle Scholar
  14. Pradet-Balade B, Boulmé F, Beug H, Müllner EW, Garcia-Sanz JA (2001) Translational control: bridging the gap between genomics and proteomics? Trends Biochem Sci 26:225–229PubMedCrossRefGoogle Scholar
  15. Rogers JC (1985) Two barley α-amylase gene families are regulated differently in aleurone cells. J Biol Chem 260:3731–3738PubMedGoogle Scholar
  16. Shen L, Gong J, Caldo RA, Nettleton D, Cook D, Wise RP, Dickerson JA (2005) BarleyBase-an expression profiling database for plant genomics. Nucleic Acids Res 33: Database issueGoogle Scholar
  17. Skadsen RW (1993) Aleurones from a barley with low α-amylase activity become highly responsive to gibberellin when detached from the starchy endosperm. Plant Physiol 102:195–203PubMedGoogle Scholar
  18. Skadsen RW, Scandalios JG (1986) Evidence for processing of maize catalase 2 and purification of its messenger RNA aided by translation of antibody-bound polysomes. Biochemistry 25:2027–2032PubMedCrossRefGoogle Scholar
  19. Skadsen RW, Tibbot BK (1994) Temporal expression patterns of Alpha-amylase isozymal genes in polysomal and total RNAs of germinating barleys. J Cereal Sci 19:199–208CrossRefGoogle Scholar
  20. Skadsen RW, Schulze-Lefert P, Herbst JM (1995) Molecular cloning, characterization and expression analysis of two catalase isozymal genes in barley. Plant Mol. Biol 29:1005–1014PubMedCrossRefGoogle Scholar
  21. Svensson JT, Crosatti C, Campoli C, Bassi R, Stanca AM, Close TJ, Cattivelli L (2006) Transcriptome analysis of cold acclimation in barley Albina and Xantha mutants. Plant Physiol 141:257–270PubMedCrossRefGoogle Scholar
  22. Tusher VG, Tibshirani R, Chu G (2001) Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA 98:5116–5121PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2007

Authors and Affiliations

  1. 1.USDA/ARS Cereal Crops Research UnitMadisonUSA

Personalised recommendations