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Functional & Integrative Genomics : Volume 7, Issue 2, April 2007

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

Content Provider	Springer Nature Link
Author	Poole, Rebecca Barker, Gary Wilson, Ian D. Coghill, Jane A. Edwards, Keith J.
Copyright Year	2007
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.
Starting Page	207
Ending Page	219
Page Count	13
File Format	PDF
ISSN	1438793X
Journal	Functional & Integrative Genomics
Volume Number	7
Issue Number	3
e-ISSN	14387948
Language	English
Publisher	Springer-Verlag
Publisher Date	2007-03-16
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Triticum aestivum Affymetrix GeneChip array cDNA microarrays Polyploids Animal Genetics and Genomics Bioinformatics Biochemistry Microbial Genetics and Genomics Plant Genetics & Genomics Cell Biology
Content Type	Text
Resource Type	Article
Subject	Genetics Medicine

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