A rapid RNA extraction method from oil palm tissues suitable for reverse transcription quantitative real-time PCR (RT-qP
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ORIGINAL ARTICLE
A rapid RNA extraction method from oil palm tissues suitable for reverse transcription quantitative real‑time PCR (RT‑qPCR) Siti Suriawati Badai1 · Omar Abd Rasid1 · Ghulam Kadir Ahmad Parveez1 · Mat Yunus Abdul Masani1 Received: 19 May 2020 / Accepted: 27 October 2020 © King Abdulaziz City for Science and Technology 2020
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. Keywords Oil palm · RNA extraction protocol · Cetyltrimethylammonium bromide · Silica column · RT-qPCR
Introduction Oil palm is a major tropical oil crop worldwide. Global production of palm oil is around 70.5 million metric tons in the marketing year 2018/2019 (Kushairi et al. 2019). The demand for palm oil will be triple in the year 2050, exceeding 250 million metric tons (Zulkifli et al. 2017). About 90% of palm oil is used for industrial frying applications, shortenings, margarine and confectionary fats (Noor Lida et al. 2017). The remaining 10% of palm oil is used for soap and oleochemical manufacturing (Lai et al. 2012). Palm oil is favoured by the food industry because of its competitive price, excellent oxidative stability, high nutritional value, free of trans fatty acids and rich with antioxidant properties (Ong and Goh 2002; Noor Lida et al. 2017). In order to fulfil the strong demand for the palm oil, yield and quality of Electronic supplementary material The online version of this article (https://doi.org/10.1007/s13205-020-02514-9) contains supplementary material, which is available to authorized users. * Mat Yunus Abdul Masani [email protected] 1
Advanced Biotechnology and Breeding Centre (ABBC) Division, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor, Malaysia
palm oil are being improved through various efforts including plant biotechnology approach (Parveez et al. 2015a; Masura et al. 2017; Masani et al. 2018). RNA sequencing (RNA-Seq) is an indispensable tool to analyse the continuously changing cellular transcriptome using next-generation sequencing (NGS) (Hrdlickova et al. 2017). Reverse transcription quantitative real-time PCR (RT-qPCR) is a lab
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