Analysis of multiple transcriptomes of the African oil palm (Elaeis guineensis) to identify reference genes for RT-qPCR

Xia, Wei, Mason, Annaliese S., Xiao, Yong, Liu, Zheng, Yang, Yaodong, Lei, Xintao, Wu, Xiaoming, Ma, Zilong and Peng, Ming (2014) Analysis of multiple transcriptomes of the African oil palm (Elaeis guineensis) to identify reference genes for RT-qPCR. Journal of Biotechnology, 184 63-73. doi:10.1016/j.jbiotec.2014.05.008

Author Xia, Wei
Mason, Annaliese S.
Xiao, Yong
Liu, Zheng
Yang, Yaodong
Lei, Xintao
Wu, Xiaoming
Ma, Zilong
Peng, Ming
Title Analysis of multiple transcriptomes of the African oil palm (Elaeis guineensis) to identify reference genes for RT-qPCR
Journal name Journal of Biotechnology   Check publisher's open access policy
ISSN 0168-1656
Publication date 2014-08-20
Sub-type Article (original research)
DOI 10.1016/j.jbiotec.2014.05.008
Open Access Status DOI
Volume 184
Start page 63
End page 73
Total pages 11
Place of publication Amsterdam, The Netherlands
Publisher Elsevier
Language eng
Subject 1305 Biotechnology
2402 Applied Microbiology and Biotechnology
Abstract The African oil palm (Elaeis guineensis), which is grown in tropical and subtropical regions, is a highly productive oil-bearing crop. For gene expression-based analyses such as reverse transcription-quantitative real time PCR (RT-qPCR), reference genes are essential to provide a baseline with which to quantify relative gene expression. Normalization using reliable reference genes is critical in correctly interpreting expression data from RT-qPCR. In order to identify suitable reference genes in African oil palm, 17 transcriptomes of different tissues obtained from NCBI were systematically assessed for gene expression variation. In total, 53 putative candidate reference genes with coefficient of variation values <3.0 were identified: 18 in reproductive tissue and 35 in vegetative tissue. Analysis for enriched functions showed that approximately 90% of identified genes were clustered in cell component gene functions, and 12 out of 53 genes were traditional housekeeping genes. We selected and validated 16 reference genes chosen from leaf tissue transcriptomes by using RT-qPCR in sets of cold, drought and high salinity treated samples, and ranked expression stability using statistical algorithms geNorm, Normfinder and Bestkeeper. Genes encoding actin, adenine phosphoribosyltransferase and eukaryotic initiation factor 4A genes were the most stable genes over the cold, drought and high salinity stresses. Identification of stably expressed genes as reference gene candidates from multiple transcriptome datasets was found to be reliable and efficient, and some traditional housekeeping genes were more stably expressed than others. We provide a useful molecular genetic resource for future gene expression studies in African oil palm, facilitating molecular genetics approaches for crop improvement in this species.
Keyword Elaeis guineensis
Reference gene
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID 31101179
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Centre for Integrative Legume Research Publications
School of Agriculture and Food Sciences
Official 2015 Collection
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