Selection of low-variance expressed Malus x domestica (apple) genes for use as quantitative PCR reference genes (housekeepers)

Bowen, Judith, Ireland, Hilary S., Crowhurst, Ross, Luo, Zhiwei, Watson, Amy E., Foster, Toshi, Gapper, Nigel, Giovanonni, Jim J., Mattheis, James P., Watkins, Chris, Rudell, David, Johnston, Jason W. and Schaffer, Robert J. (2014) Selection of low-variance expressed Malus x domestica (apple) genes for use as quantitative PCR reference genes (housekeepers). Tree Genetics and Genomes, 10 3: 751-759. doi:10.1007/s11295-014-0720-6


Author Bowen, Judith
Ireland, Hilary S.
Crowhurst, Ross
Luo, Zhiwei
Watson, Amy E.
Foster, Toshi
Gapper, Nigel
Giovanonni, Jim J.
Mattheis, James P.
Watkins, Chris
Rudell, David
Johnston, Jason W.
Schaffer, Robert J.
Title Selection of low-variance expressed Malus x domestica (apple) genes for use as quantitative PCR reference genes (housekeepers)
Formatted title
Selection of low-variance expressed Malus x domestica (apple) genes for use as quantitative PCR reference genes (housekeepers)
Journal name Tree Genetics and Genomes   Check publisher's open access policy
ISSN 1614-2942
1614-2950
Publication date 2014-06
Sub-type Article (original research)
DOI 10.1007/s11295-014-0720-6
Open Access Status Not Open Access
Volume 10
Issue 3
Start page 751
End page 759
Total pages 9
Place of publication Heidelberg, Germany
Publisher Springer Verlag
Language eng
Formatted abstract
To accurately measure gene expression using PCR-based approaches, there is the need for reference genes that have low variance in expression (housekeeping genes) to normalise the data for RNA quantity and quality. For non-model species such as Malus x domestica (apples), previously, the selection of reference genes relied on using homology to reference genes in model species. In this study, a genomics approach was used to identify apple genes with low variance in expression in 217 messenger RNA (mRNA)-seq data sets covering different tissues, during fruit development, and treated with a range of different stress conditions. Ten potential reference genes were chosen for validation by quantitative PCR (qPCR) over 29 different tissue types and treatments. From the combined mRNA-seq and qPCR results, three potential reference genes are proposed that can be used as good controls for PCR based expression studies. The three genes show homology to lipid transfer proteins, phytochrome protein phosphatase and the ubiquitination pathway. With the progression of research away from non-model species, this approach provides a robust method for selecting candidate genes for use as reference genes in qPCR.
Keyword mRNA-seq
Malus x domestica
qPCR
Reference genes
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
Collection: Queensland Alliance for Agriculture and Food Innovation
 
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Created: Wed, 17 Feb 2016, 14:12:09 EST by Amy Watson on behalf of Qld Alliance for Agriculture and Food Innovation