EgRBP42 encoding an hnRNP-like RNA-binding protein from Elaeis guineensis Jacq. is responsive to abiotic stresses

Yeap, Wan-Chin; Ooi, Tony Eng Keong; Namasivayam, Parameswari; Kulaveerasingam, Harikrishna; Ho, Chai Ling

doi:10.1007/s00299-012-1297-x

Cited by 20 publications

(19 citation statements)

References 42 publications

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“…As there is increasing evidence that these genes are not consistently expressed in certain plant species or experimental conditions [20], [29], [30], other genes have been investigated on their potential as reference genes. This resulted in the application of gibberellin-responsive protein 2 ( GRAS ), cyclophilin 2 ( CYP2 ) and pre-mRNA splicing factor 7 ( SLU7 ) as reference genes in the study of oil palm leaf discs subjected to various abiotic stresses [31]. These genes also showed the most stable expression across reproductive and vegetative tissues of oil palm [32].…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Reference Genes for Quantitative Real-Time PCR in Oil Palm Elite Planting Materials Propagated by Tissue Culture

et al. 2014

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BackgroundThe somatic embryogenesis tissue culture process has been utilized to propagate high yielding oil palm. Due to the low callogenesis and embryogenesis rates, molecular studies were initiated to identify genes regulating the process, and their expression levels are usually quantified using reverse transcription quantitative real-time PCR (RT-qPCR). With the recent release of oil palm genome sequences, it is crucial to establish a proper strategy for gene analysis using RT-qPCR. Selection of the most suitable reference genes should be performed for accurate quantification of gene expression levels.ResultsIn this study, eight candidate reference genes selected from cDNA microarray study and literature review were evaluated comprehensively across 26 tissue culture samples using RT-qPCR. These samples were collected from two tissue culture lines and media treatments, which consisted of leaf explants cultures, callus and embryoids from consecutive developmental stages. Three statistical algorithms (geNorm, NormFinder and BestKeeper) confirmed that the expression stability of novel reference genes (pOP-EA01332, PD00380 and PD00569) outperformed classical housekeeping genes (GAPDH, NAD5, TUBULIN, UBIQUITIN and ACTIN). PD00380 and PD00569 were identified as the most stably expressed genes in total samples, MA2 and MA8 tissue culture lines. Their applicability to validate the expression profiles of a putative ethylene-responsive transcription factor 3-like gene demonstrated the importance of using the geometric mean of two genes for normalization.ConclusionsSystematic selection of the most stably expressed reference genes for RT-qPCR was established in oil palm tissue culture samples. PD00380 and PD00569 were selected for accurate and reliable normalization of gene expression data from RT-qPCR. These data will be valuable to the research associated with the tissue culture process. Also, the method described here will facilitate the selection of appropriate reference genes in other oil palm tissues and in the expression profiling of genes relating to yield, biotic and abiotic stresses.

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Section: Introductionmentioning

confidence: 99%

Evaluation of Reference Genes for Quantitative Real-Time PCR in Oil Palm Elite Planting Materials Propagated by Tissue Culture

et al. 2014

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“…High expression in active tissues has been a major factor the preference of GRAS as a reference gene. Yeap et al (2012) found that Cyp2 and GRAS are highly stable and preferred as reference genes as they are not affected by abiotic stressed conditions including salinity, drought, submergence, cold and heat stresses in leaf discs.…”

Section: Discussionmentioning

confidence: 99%

“…Six candidate reference genes, Cyp2, GRAS, EgEfa1, F-box, and GLU were selected from literature review (Yeap et al, 2013) for evaluation of expression stability. A conventional housekeeping gene, actin (Ooi et al, 2012), commonly used as internal control in gene expression studies was also evaluated. Primer sequences for the candidate reference genes are as listed in Table 1.…”

Section: Candidate Gene Selection and Primer Designmentioning

confidence: 99%

“…There are several genes including cyclophilin 2 (Cyp2), glutaredoxin (GLU) and gibberellinresponsive protein 2 (GRAS) that have been used as reference genes in oil palm studies (Lim et al, 2017;Kwan et al, 2016;Xia et al, 2014;Yeap et al, 2012). Normalisation in studies on basal cell metabolism, cytoskeletons, and intracellular functions previously used conventional housekeeping genes including glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin, 18S and 28S ribosomal RNA for internal control (Li et al, 2017;Thuc et al, 2011;Zheng and Sun, 2011).…”

Section: Introductionmentioning

confidence: 99%

“…This study reports on the selection of suitable reference genes for gene expression profiling using qRT-PCR in oil palm. In this study, six candidate reference genes obtained from previous studies (Yeap et al, 2013) and transcriptome results (Ooi et al, 2012), namely actin, Cyp2, GRAS, EgEfa1, F-box, and GLU were evaluated using two statistical software for selection of qRT-PCR reference genes in oil palm studies based on their stability.…”

Section: Introductionmentioning

confidence: 99%

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Identification of Reliable Reference Genes for Gene Expression Studies of Oil Palm Plantlets Using Normfinder and Bestkeeper Algorithms

H¹

2019

JOPR

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Gene expression profiling analysis using real-time quantitative polymerase chain reaction (qRT-PCR) is commonly used due to its reliability and accuracy. Gene expression profiles of particular genes in different tissues and developmental stages aid in the understanding of their biological functions. However, the accuracy and reliability of qRT-PCR to study gene expression demand the use of species-specific reference genes for normalisation. Therefore, appropriate reference genes for qRT-PCR need to be determined for oil palm (Elaeis guineensis) tissues. In this study, six candidate reference genes namely actin, Cyp2, GRAS, EgEfa1, F-box, and GLU were examined in leaf, node, internode, root, cabbage, shoot primordial and basal stem tissues of two-year old clonal oil palms. Two statistical algorithms, NormFinder and BestKeeper verified the stability of GRAS and Cyp2 reference genes in the oil palm tissues tested. The combination of Cyp2 and GRAS reference genes are recommended for gene expression normalisation profiles in nurserystage oil palm plantlets.

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Palms in an ‘Omics’ Era

Arunachalam

2021

The Coconut Genome

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EgRBP42 encoding an hnRNP-like RNA-binding protein from Elaeis guineensis Jacq. is responsive to abiotic stresses

Cited by 20 publications

References 42 publications

Evaluation of Reference Genes for Quantitative Real-Time PCR in Oil Palm Elite Planting Materials Propagated by Tissue Culture

Evaluation of Reference Genes for Quantitative Real-Time PCR in Oil Palm Elite Planting Materials Propagated by Tissue Culture

Identification of Reliable Reference Genes for Gene Expression Studies of Oil Palm Plantlets Using Normfinder and Bestkeeper Algorithms

Palms in an ‘Omics’ Era

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