Designing gRNAs targeting oil palm phytoene desaturase (EgPDS) gene and construction of vectors for oil palm CRISPR/Cas9 study
The CRISPR/Cas9 system is a precise and versatile genetic tool used to induce site-specific manipulation in the targeted gene. This study elaborates on the strategy to select the gRNAs targeting the oil palm phytoene desaturase (EgPDS) gene, which complements CRISPR-GE and sequence analysis. Sixty-o...
| Main Authors: | , , , , , , |
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| Format: | Article |
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Malaysian Palm Oil Board
2022
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| Online Access: | http://psasir.upm.edu.my/id/eprint/100905/ |
| _version_ | 1848863444039630848 |
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| author | Jamaludin, Norfaezah Bahariah, Bohari Shaharuddin, Noor Azmi Chai, Ling Ho Abdul Rasid, Omar Ahmad Parveez, Ghulam Kadir Abdul Masani, Mat Yunus |
| author_facet | Jamaludin, Norfaezah Bahariah, Bohari Shaharuddin, Noor Azmi Chai, Ling Ho Abdul Rasid, Omar Ahmad Parveez, Ghulam Kadir Abdul Masani, Mat Yunus |
| author_sort | Jamaludin, Norfaezah |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | The CRISPR/Cas9 system is a precise and versatile genetic tool used to induce site-specific manipulation in the targeted gene. This study elaborates on the strategy to select the gRNAs targeting the oil palm phytoene desaturase (EgPDS) gene, which complements CRISPR-GE and sequence analysis. Sixty-one gRNAs were selected from 167 gRNA candidates generated by the CRISPR-GE tool. These gRNA candidates were further analysed to meet the specific criteria, including the guanine (G) and cytosine (C) content of 35%-60% and the presence of preferable gRNA features. From 61 gRNAs, seven gRNAs were selected, which represent three different parts of the EgPDS gene in the genome. The efficiency of each gRNA candidate to cause cleavage on the target gene was confirmed by in vitro cleavage analysis. All seven gRNA candidates were then cloned into the pYLsgRNA-OsU6 cassette before being incorporated seamlessly into the final transformation vector, pYLCRISPR/Cas9P35S-H, via Gibson assembly. Three CRISPR/Cas9 transformation vectors targeting the EgPDS gene, namely pYLEgPDS1-35S-H, pYLEgPDS2-35S-H and pYLEgPDS3-35S-H, were successfully constructed. These constructs will be transformed into oil palm protoplasts via polyethylene glycol (PEG)- mediated transformation and subsequently into oil palm embryogenic calli via biolistic and Agrobacteriummediated transformation to determine the efficacy of the multiplex CRISPR/Cas9 system in oil palm genome. |
| first_indexed | 2025-11-15T13:33:01Z |
| format | Article |
| id | upm-100905 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| last_indexed | 2025-11-15T13:33:01Z |
| publishDate | 2022 |
| publisher | Malaysian Palm Oil Board |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-1009052023-07-14T04:04:33Z http://psasir.upm.edu.my/id/eprint/100905/ Designing gRNAs targeting oil palm phytoene desaturase (EgPDS) gene and construction of vectors for oil palm CRISPR/Cas9 study Jamaludin, Norfaezah Bahariah, Bohari Shaharuddin, Noor Azmi Chai, Ling Ho Abdul Rasid, Omar Ahmad Parveez, Ghulam Kadir Abdul Masani, Mat Yunus The CRISPR/Cas9 system is a precise and versatile genetic tool used to induce site-specific manipulation in the targeted gene. This study elaborates on the strategy to select the gRNAs targeting the oil palm phytoene desaturase (EgPDS) gene, which complements CRISPR-GE and sequence analysis. Sixty-one gRNAs were selected from 167 gRNA candidates generated by the CRISPR-GE tool. These gRNA candidates were further analysed to meet the specific criteria, including the guanine (G) and cytosine (C) content of 35%-60% and the presence of preferable gRNA features. From 61 gRNAs, seven gRNAs were selected, which represent three different parts of the EgPDS gene in the genome. The efficiency of each gRNA candidate to cause cleavage on the target gene was confirmed by in vitro cleavage analysis. All seven gRNA candidates were then cloned into the pYLsgRNA-OsU6 cassette before being incorporated seamlessly into the final transformation vector, pYLCRISPR/Cas9P35S-H, via Gibson assembly. Three CRISPR/Cas9 transformation vectors targeting the EgPDS gene, namely pYLEgPDS1-35S-H, pYLEgPDS2-35S-H and pYLEgPDS3-35S-H, were successfully constructed. These constructs will be transformed into oil palm protoplasts via polyethylene glycol (PEG)- mediated transformation and subsequently into oil palm embryogenic calli via biolistic and Agrobacteriummediated transformation to determine the efficacy of the multiplex CRISPR/Cas9 system in oil palm genome. Malaysian Palm Oil Board 2022-03 Article PeerReviewed Jamaludin, Norfaezah and Bahariah, Bohari and Shaharuddin, Noor Azmi and Chai, Ling Ho and Abdul Rasid, Omar and Ahmad Parveez, Ghulam Kadir and Abdul Masani, Mat Yunus (2022) Designing gRNAs targeting oil palm phytoene desaturase (EgPDS) gene and construction of vectors for oil palm CRISPR/Cas9 study. Journal of Oil Palm Research, 35 (1). pp. 133-146. ISSN 2811-4701 http://jopr.mpob.gov.my/designing-grnas-targeting-oil-palm-phytoene-desaturase-iegpdsi-gene-and-construction-of-vectors-for-oil-palm-crisprcas9-study/ 10.21894/jopr.2022.0032 |
| spellingShingle | Jamaludin, Norfaezah Bahariah, Bohari Shaharuddin, Noor Azmi Chai, Ling Ho Abdul Rasid, Omar Ahmad Parveez, Ghulam Kadir Abdul Masani, Mat Yunus Designing gRNAs targeting oil palm phytoene desaturase (EgPDS) gene and construction of vectors for oil palm CRISPR/Cas9 study |
| title | Designing gRNAs targeting oil palm phytoene desaturase (EgPDS) gene and construction of vectors for oil palm CRISPR/Cas9 study |
| title_full | Designing gRNAs targeting oil palm phytoene desaturase (EgPDS) gene and construction of vectors for oil palm CRISPR/Cas9 study |
| title_fullStr | Designing gRNAs targeting oil palm phytoene desaturase (EgPDS) gene and construction of vectors for oil palm CRISPR/Cas9 study |
| title_full_unstemmed | Designing gRNAs targeting oil palm phytoene desaturase (EgPDS) gene and construction of vectors for oil palm CRISPR/Cas9 study |
| title_short | Designing gRNAs targeting oil palm phytoene desaturase (EgPDS) gene and construction of vectors for oil palm CRISPR/Cas9 study |
| title_sort | designing grnas targeting oil palm phytoene desaturase (egpds) gene and construction of vectors for oil palm crispr/cas9 study |
| url | http://psasir.upm.edu.my/id/eprint/100905/ http://psasir.upm.edu.my/id/eprint/100905/ http://psasir.upm.edu.my/id/eprint/100905/ |