Plant Salt Tolerance pp 335-350

Part of the Methods in Molecular Biology book series (MIMB, volume 913) | Cite as

Transcriptomics on Small Samples

  • Stuart J. Roy
  • Simon J. Conn
  • Gwenda M. Mayo
  • Asmini Athman
  • Matthew Gilliham


Interrogating the cell-specific transcriptome forms an important component of understanding the role that specific cells play in assisting a plant to overcome abiotic stress. Among the challenges arising when extracting RNA from individual plant cells are: the isolation of pure cell populations; the small yield of material when isolating specific cell types, and ensuring an accurate representation of the transcriptome from each cell type after amplification of RNA. Here we describe two approaches for isolating RNA from specific cell types—single cell sampling and analysis (SiCSA) and laser capture microdissection. Isolated RNA can then be directly sampled qualitatively using reverse transcription PCR (RT-PCR) or amplified for profiling ­multiple specific genes using quantitative RT-PCR and genome-wide transcript analyses.

Key words

Single cell sampling and analysis (SiCSA) Laser capture microdissection Transcriptome RNA isolation 


  1. 1.
    Conn S, Gilliham M (2010) Comparative physiology of elemental distributions in plants. Ann Bot 105:1081–1102PubMedCrossRefGoogle Scholar
  2. 2.
    Galbraith DW, Birnbaum K (2006) Global studies of cell type-specific gene expression in plants. Annu Rev Plant Biol 57:451–475PubMedCrossRefGoogle Scholar
  3. 3.
    Tester M, Leigh RA (2001) Partitioning of nutrient transport processes in roots. J Exp Bot 52:445–457PubMedCrossRefGoogle Scholar
  4. 4.
    Leegood RC (1985) Intracellular compartmentation of metabolites in leaves of Zea mays L. Planta 164:163–171CrossRefGoogle Scholar
  5. 5.
    Munns R, Tester M (2008) Mechanisms of salinity tolerance. Annu Rev Plant Biol 59:651–681PubMedCrossRefGoogle Scholar
  6. 6.
    Plett DC, Skrumsager Møller I (2010) Na+ transport in glycophytic plants: what we know and would like to know. Plant Cell Environ 33:612–626CrossRefGoogle Scholar
  7. 7.
    Teakle NL, Tyerman SD (2010) Mechanisms of Cl transport contributing to salt tolerance. Plant Cell Environ 33:566–589PubMedCrossRefGoogle Scholar
  8. 8.
    Roy SJ, Gilliham M, Berger B et al (2008) Investigating glutamate receptor-like gene ­co-expression in Arabidopsis thaliana. Plant Cell Environ 31:861–871PubMedCrossRefGoogle Scholar
  9. 9.
    Conn SJ, Conn V, Tyerman SD et al (2011) Magnesium transporters, MGT2/MRS2-1 and MGT3/MRS2-5, are important for magnesium partitioning within Arabidopsis thaliana mesophyll vacuoles. New Phytol 190:583–594PubMedCrossRefGoogle Scholar
  10. 10.
    Conn SJ, Gilliham M, Athman A et al (2011) Cell-specific vacuolar calcium storage mediated by CAX1 regulates apoplastic calcium concentration, gas exchange, and plant productivity in Arabidopsis. Plant Cell 23:240–257PubMedCrossRefGoogle Scholar
  11. 11.
    Li P, Ponnala L, Gandotra N et al (2010) The developmental dynamics of the maize leaf transcriptome. Nat Genet 42:1060–1067PubMedCrossRefGoogle Scholar
  12. 12.
    Møller I, Gilliham M, Jha D et al (2009) Salinity tolerance engineered by cell type-specific over-expression of a Na+ transporter in the Arabidopsis root. Plant Cell 21:2163–2178PubMedCrossRefGoogle Scholar
  13. 13.
    Nelson T, Tausta SL, Gandotra N et al (2006) Laser microdissection of plant tissue: what you see is what you get. Annu Rev Plant Biol 57:181–201PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Stuart J. Roy
    • 1
  • Simon J. Conn
    • 2
  • Gwenda M. Mayo
    • 1
  • Asmini Athman
    • 3
  • Matthew Gilliham
    • 3
  1. 1.Australian Centre for Plant Functional Genomics and School of AgricultureFood and Wine & Waite Research InstituteGlen OsmondAustralia
  2. 2.European Molecular Biology LaboratoryGrenoble OutstationGrenobleFrance
  3. 3.School of Agriculture, Food and Wine, & Waite Research InstituteUniversity of AdelaideGlen OsmondAustralia

Personalised recommendations