Identification of oil palm root-specific genes through mining of RNA-Seq data and RT-qPCR analysis
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 discover...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
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Malaysian Palm Oil Board
2021
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| Online Access: | http://psasir.upm.edu.my/id/eprint/101773/ |
| _version_ | 1848863628769361920 |
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| author | Subhi, Siti Masura Omar, Abd Rasid Shaharuddin, Noor Azmi Abdul Masani, Mat Yunus Chan, Kuang Lim Low, Eng Ti Leslie Badai, Siti Suriawati Ayub, Nor Hanin Abdul Rahman, Siti Rahmah Abdullah, Mohd Puad Mohamad Azzeme, Azzreena Ahmad Parveez, Ghulam Kadir |
| author_facet | Subhi, Siti Masura Omar, Abd Rasid Shaharuddin, Noor Azmi Abdul Masani, Mat Yunus Chan, Kuang Lim Low, Eng Ti Leslie Badai, Siti Suriawati Ayub, Nor Hanin Abdul Rahman, Siti Rahmah Abdullah, Mohd Puad Mohamad Azzeme, Azzreena Ahmad Parveez, Ghulam Kadir |
| author_sort | Subhi, Siti Masura |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | 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 root-specific 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’ promoter’s potential to regulate a strong expression level of transgenes in a root-specific manner. |
| first_indexed | 2025-11-15T13:35:57Z |
| format | Article |
| id | upm-101773 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-15T13:35:57Z |
| publishDate | 2021 |
| publisher | Malaysian Palm Oil Board |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-1017732023-10-26T00:51:01Z http://psasir.upm.edu.my/id/eprint/101773/ Identification of oil palm root-specific genes through mining of RNA-Seq data and RT-qPCR analysis Subhi, Siti Masura Omar, Abd Rasid Shaharuddin, Noor Azmi Abdul Masani, Mat Yunus Chan, Kuang Lim Low, Eng Ti Leslie Badai, Siti Suriawati Ayub, Nor Hanin Abdul Rahman, Siti Rahmah Abdullah, Mohd Puad Mohamad Azzeme, Azzreena Ahmad Parveez, Ghulam Kadir 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 root-specific 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’ promoter’s potential to regulate a strong expression level of transgenes in a root-specific manner. Malaysian Palm Oil Board 2021-08-30 Article PeerReviewed Subhi, Siti Masura and Omar, Abd Rasid and Shaharuddin, Noor Azmi and Abdul Masani, Mat Yunus and Chan, Kuang Lim and Low, Eng Ti Leslie and Badai, Siti Suriawati and Ayub, Nor Hanin and Abdul Rahman, Siti Rahmah and Abdullah, Mohd Puad and Mohamad Azzeme, Azzreena and Ahmad Parveez, Ghulam Kadir (2021) Identification of oil palm root-specific genes through mining of RNA-Seq data and RT-qPCR analysis. Journal of Oil Palm Research, 34 (2). 261 - 275. ISSN 1511-2780 http://jopr.mpob.gov.my/identification-of-oil-palm-root-specific-genes-through-mining-of-rna-seq-data-and-rt-qpcr-analysis/ 10.21894/jopr.2021.0036 |
| spellingShingle | Subhi, Siti Masura Omar, Abd Rasid Shaharuddin, Noor Azmi Abdul Masani, Mat Yunus Chan, Kuang Lim Low, Eng Ti Leslie Badai, Siti Suriawati Ayub, Nor Hanin Abdul Rahman, Siti Rahmah Abdullah, Mohd Puad Mohamad Azzeme, Azzreena Ahmad Parveez, Ghulam Kadir Identification of oil palm root-specific genes through mining of RNA-Seq data and RT-qPCR analysis |
| title | Identification of oil palm root-specific genes through mining of RNA-Seq data and RT-qPCR analysis |
| title_full | Identification of oil palm root-specific genes through mining of RNA-Seq data and RT-qPCR analysis |
| title_fullStr | Identification of oil palm root-specific genes through mining of RNA-Seq data and RT-qPCR analysis |
| title_full_unstemmed | Identification of oil palm root-specific genes through mining of RNA-Seq data and RT-qPCR analysis |
| title_short | Identification of oil palm root-specific genes through mining of RNA-Seq data and RT-qPCR analysis |
| title_sort | identification of oil palm root-specific genes through mining of rna-seq data and rt-qpcr analysis |
| url | http://psasir.upm.edu.my/id/eprint/101773/ http://psasir.upm.edu.my/id/eprint/101773/ http://psasir.upm.edu.my/id/eprint/101773/ |