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Measuring global gene expression in polyploidy; a cautionary note from allohexaploid wheat.

Rebecca Poole1, Gary Barker, Ian D Wilson

  • 1School of Biological Sciences, University of Bristol, Bristol, UK. R.L.Poole@bristol.ac.uk

Functional & Integrative Genomics
|March 17, 2007
PubMed
Summary

Comparing gene expression platforms in polyploid wheat revealed significant discrepancies. Current methods struggle to differentiate homoeologous and paralogous gene copies, necessitating specialized arrays for accurate polyploid gene expression studies.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Plant Science

Background:

  • Global gene expression studies are increasing, with an assumption of similar results across platforms.
  • Polyploid organisms, like hexaploid wheat, present unique challenges due to homoeologous and paralogous gene copies.

Purpose of the Study:

  • To compare gene expression profiling of hexaploid wheat using three distinct platforms: Affymetrix GeneChip Wheat Genome Array, a custom complementary DNA array, and quantitative reverse transcription-polymerase chain reaction (qRT-PCR).
  • To investigate inter-platform discrepancies and their causes in polyploid gene expression analysis.

Main Methods:

  • Gene expression analysis of hexaploid wheat using Affymetrix GeneChip Wheat Genome Array.
  • Gene expression analysis using an in-house custom-spotted complementary DNA array.

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  • Gene expression analysis using quantitative reverse transcription-polymerase chain reaction (qRT-PCR).
  • Comparative analysis of data generated from the three platforms.

    • Main Results:

    • Little concordance was observed between the gene expression platforms, indicating global comparisons are not feasible.
    • Inter-platform discrepancies were attributed to the inability of platforms to discriminate between related transcripts.
    • Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) showed variable discriminatory ability, impacting validation accuracy in polyploid studies.

    Conclusions:

    • Standard gene expression platforms exhibit poor concordance in polyploid organisms.
    • The inability to distinguish homoeologous and paralogous transcripts is a major limitation.
    • Development and use of homoeologous- and paralogous-specific arrays are crucial for accurate polyploid gene expression studies.