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A rapid RNA extraction method from oil palm tissues suitable for reverse transcription quantitative real-time PCR (RT-qPCR)

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Abstract

Cetyltrimethylammonium bromide (CTAB) is the preferred detergent in RNA extraction of oil palm tissues. However, the CTAB-based protocol is time-consuming. In this study, a combination of the CTAB-based method and silica-based purification reduced the extraction time from two days to five hours. Quality of total RNA from 27 different tissues of oil palm was shown to have an RNA integrity number (RIN) value of more than seven. The extracted RNA was evaluated by RT-qPCR using three reference oil palm genes (GRAS, CYP2, and SLU7) and three putative mesocarp-specific transcripts annotated as WRKY DNA-binding protein 70 (WRKY-70), metallothionein (MT) and pentatricopeptide repeat (PPR) genes. Tissue-specific expression profiling across complete developmental stages of mesocarp and vegetative tissues was determined in this study. Overall, the RNA extraction protocol described here is rapid, simple and yields good quality RNAs from oil palm tissues.

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Acknowledgements

The authors would like to thank the MPOB management for permission to publish this work. We would also like to acknowledge the members of Transgenic Technology Group (TTG) for their technical assistance. We thank Breeding and Tissue Culture Unit for providing mesocarp tissues from five weeks after anthesis (WAA) to 20 WAA and oil palm tissue culture materials (embryogenic callus, polyembryoid and plantlet).

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Authors and Affiliations

  1. Advanced Biotechnology and Breeding Centre (ABBC) Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia

    Siti Suriawati Badai, Omar Abd Rasid, Ghulam Kadir Ahmad Parveez & Mat Yunus Abdul Masani

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  1. Siti Suriawati Badai
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  2. Omar Abd Rasid
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  3. Ghulam Kadir Ahmad Parveez
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  4. Mat Yunus Abdul Masani
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Contributions

BSS established the protocol and drafted the manuscript. ROA, PGKA and MMYA initiated and guided the project, and revised the manuscript.

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Correspondence to Mat Yunus Abdul Masani.

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The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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Badai, S.S., Rasid, O.A., Parveez, G.K.A. et al. A rapid RNA extraction method from oil palm tissues suitable for reverse transcription quantitative real-time PCR (RT-qPCR). 3 Biotech 10, 530 (2020). https://doi.org/10.1007/s13205-020-02514-9

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