title: Analysis of multiple transcriptomes of the African oil palm (Elaeis guineensis) to identify reference genes for RT-qPCR.
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.
authors.affiliation: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339, PR China. Electronic address: zjxiawei@gmail.com.
authors.forename: Wei
authors.initials: W
authors.lastname: Xia
authors.affiliation: School of Agriculture and Food Sciences and Centre for Integrative Legume Research, The University of Queensland, 4072 Brisbane, Australia.
authors.forename: Annaliese S
authors.initials: AS
authors.lastname: Mason
authors.affiliation: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339, PR China.
authors.forename: Yong
authors.initials: Y
authors.lastname: Xiao
authors.affiliation: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339, PR China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Liu
authors.affiliation: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339, PR China.
authors.forename: Yaodong
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Hainan Key Laboratory of Tropical Oil Crops Biology/Coconuts Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan 571339, PR China.
authors.forename: Xintao
authors.initials: X
authors.lastname: Lei
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Institute of Oil Crops Biology, Chinese Academy of Agricultural Sciences, Wuhan 430070, PR China.
authors.forename: Xiaoming
authors.initials: X
authors.lastname: Wu
authors.affiliation: MOA Key Laboratory of Tropical Crop Biology and Genetic Resources Utilization, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, PR China.
authors.forename: Zilong
authors.initials: Z
authors.lastname: Ma
authors.affiliation: MOA Key Laboratory of Tropical Crop Biology and Genetic Resources Utilization, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, PR China.
authors.forename: Ming
authors.initials: M
authors.lastname: Peng
mesh_terms: D000465:Algorithms; D028023:Arecaceae / Q000235:genetics* / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D000073878:Palm Oil; D018515:Plant Leaves / Q000235:genetics; D010938:Plant Oils; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods*; D012015:Reference Standards; D059467:Transcriptome / Q000235:genetics*
chemical_list: D010938:Plant Oils; D000073878:Palm Oil
keywords: Elaeis guineensis; RT-qPCR; Reference gene; Transcriptomes