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

RL Poole, GLA Barker, ID Wilson, JA Coghill, KJ Edwards

Research output: Contribution to journalArticle (Academic Journal)peer-review

24 Citations (Scopus)

Abstract

The number of global gene expression studies has increased significantly in recent years. It is assumed that the different techniques employed report similar levels of gene expression for each sequence type. While this may be true for many species, polyploids containing homoeologous and paralogous gene copies represent a unique situation. In this paper, we describe the comparison of the Affymetrix GeneChip® Wheat Genome Array, an in-house custom-spotted complementary DNA array and quantitative reverse transcription-polymerase chain reaction (PCR) for the study of gene expression in hexaploid wheat. Analysis of the data generated from each platform revealed little concordance and suggested that global comparisons are not possible. Potential causes of these inter-platform discrepancies were investigated and revealed to be due to the inability of the platforms to discriminate between different but related transcripts. Our results also showed that the traditionally used array validation technique, quantitative reverse transcription PCR, differs in its discriminatory ability, resulting in the poor confirmation rates seen in previous polyploid studies. These findings have implications for gene expression studies in polyploid organisms and highlight the need for homoeologous- and paralogous-specific arrays when investigating polyploid gene expression.
Translated title of the contributionMeasuring global gene expression in polypoidy; a cautionary note from allohexaploid wheat
Original languageEnglish
Pages (from-to)207 - 219
Number of pages13
JournalFunctional and Integrative Genomics
Volume7 (3)
DOIs
Publication statusPublished - Jul 2007

Bibliographical note

Publisher: Springer

Fingerprint

Dive into the research topics of 'Measuring global gene expression in polypoidy; a cautionary note from allohexaploid wheat'. Together they form a unique fingerprint.

Cite this