Identification of oil palm root-specific genes through mining of RNA-seq data and RT-qPCR analysis

Mohd Puad Abdullah, . and Abdul Masani Mat Yunus, . and Nor Hanin Ayub, . and Siti Rahmah Abdul Rahman, . and Low Leslie Eng-Ti, . and Chan Kuang-Lim, . and Siti Suriawati Badai, . and Ghulam Kadir Ahmad Parveez, . and Abd Rasid Omar, . and Siti Masura Subhi, . and Azzreena Mohamad Azzeme, . and Noor Azmi Shaharuddin, . Identification of oil palm root-specific genes through mining of RNA-seq data and RT-qPCR analysis. pp. 261-275. ISSN 2811-4701

Identification of novel genes that are specifically expressed in root is essential for isolation and characterisation of root-specific promoters. Mining the transcriptome of various oil palm tissue-specific data generated from ribonucleic acid-sequencing (RNA-Seq) technology has enabled the discovery of rootspecific genes. A total of seven candidates of root-specifically or preferentially expressed genes were selected from RNA-Seq analysis and the gene expression profiles were validated using real-time quantitative polymerase chain reaction (RT-qPCR). The relative fold change of transcript expression in RT-qPCR was statistically analysed by comparing with root tissues at the in vitro culture stage (RS1). Results showed that the transcript annotated as an oil palm metallothionine (EgMT) gene was significantly upregulated at around 7 to 170-fold across the different developmental stages of root tissues. A proline-rich protein (EgPRP1) transcript was also significantly upregulated by about 7 to 55-fold. Both EgMT and EgPRP1 transcripts had relatively low expressions in the other tissues studied. The high levels of expression of EgMT and EgPRP1 in roots highlighted the genes promoters potential to regulate a strong expression level of transgenes in a root-specific manner.

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Abstract

Identification of novel genes that are specifically expressed in root is essential for isolation and characterisation of root-specific promoters. Mining the transcriptome of various oil palm tissue-specific data generated from ribonucleic acid-sequencing (RNA-Seq) technology has enabled the discovery of rootspecific genes. A total of seven candidates of root-specifically or preferentially expressed genes were selected from RNA-Seq analysis and the gene expression profiles were validated using real-time quantitative polymerase chain reaction (RT-qPCR). The relative fold change of transcript expression in RT-qPCR was statistically analysed by comparing with root tissues at the in vitro culture stage (RS1). Results showed that the transcript annotated as an oil palm metallothionine (EgMT) gene was significantly upregulated at around 7 to 170-fold across the different developmental stages of root tissues. A proline-rich protein (EgPRP1) transcript was also significantly upregulated by about 7 to 55-fold. Both EgMT and EgPRP1 transcripts had relatively low expressions in the other tissues studied. The high levels of expression of EgMT and EgPRP1 in roots highlighted the genes promoters potential to regulate a strong expression level of transgenes in a root-specific manner.

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Item Type:	Article
AGROVOC Term:	Oil palm
AGROVOC Term:	Elaeis guineensis
AGROVOC Term:	Genes
AGROVOC Term:	Ribonucleic acid
AGROVOC Term:	RNA sequence
AGROVOC Term:	Polymerase chain reaction
AGROVOC Term:	Identification
Depositing User:	Mr. AFANDI ABDUL MALEK
Last Modified:	24 Apr 2025 00:55
URI:	http://webagris.upm.edu.my/id/eprint/10676

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