In silico development of CRISPR/Cas9 construct for oryza sativa subsp. indica

Md Yusof, Anis Afuza and Abdul Sattar, Siti Syafiqa and Mohd Zim, Nurul Asyikin and Abdul Hamid, Azzmer Azzar and Zainuddin, Zarina and Samsulrizal, Nurul Hidayah (2021) In silico development of CRISPR/Cas9 construct for oryza sativa subsp. indica. In: 7th International Conference on Advancement in Science and Technology (iCAST2021)., 24-26 Aug 2021, Virtual Seminar. (Unpublished)

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Abstract

Oryza sativa, which is commonly known as rice, is one of the staple foods consumed by Asian. There are three subspecies of O. sativa that are different in their geographical adaptations which are Japonica, Javanica and Indica. Climate change causes increasing greenhouse gas emissions fluctuating rainfall, and drought which is the limiting factors of rice production in Malaysia. In rice, SUMO E2-Conjugating Enzyme (OsSCE1) gene plays a role as a negative regulator in the drought stress response. OsSCE1 gene is a type of small ubiquitin-like modifier (SUMO)-conjugating enzyme involved in a few regulatory processes such as SUMOylation. The crop improvement can be made possible through a genome editing approach which enables the manipulation of targeted genetic traits and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system is one of the genomes editing technologies that are accessible. In this study, the CRISPR construct of drought tolerance of Oryza sativa subsp. indica was developed. The CRISPR construct development involved several stages; OsSCE1 gene prediction, sgRNA design, and vector construction. FGENESH and GeneMarkS were used for OsSCE1 gene prediction. The predicted OsSCE1 gene has been validated using Polymerisation Chain Reaction (PCR) and sequencing. The BLASTN result shows high similarity with Oryza sativa in chromosome 10 with 99% identities. This step followed by sgRNA design which was carried out manually with the help of gRNA prediction tools such as WU-CRISPR, CCTop, Benchling, and CRISPR-P. Lastly, vector construction was executed virtually using Benchling. Overall, the OsSCE1 gene was successfully characterized and validated, and the in silico CRISPR construct for Oryza sativa subsp. indica was developed. To ensure a good outcome, in silico CRISPR construct should be verified through in vivo studies in further.

Item Type:	Conference or Workshop Item (Slide Presentation)
Additional Information:	8022/92864
Subjects:	Q Science > Q Science (General)
Kulliyyahs/Centres/Divisions/Institutes (Can select more than one option. Press CONTROL button):	Kulliyyah of Science > Department of Plant Science Kulliyyah of Science
Depositing User:	Dr Nurul Hidayah Samsulrizal
Date Deposited:	13 Oct 2021 10:41
Last Modified:	13 Oct 2021 10:41
URI:	http://irep.iium.edu.my/id/eprint/92864

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• In silico development of CRISPR/Cas9 construct for oryza sativa subsp. indica. (deposited 13 Oct 2021 10:41) [Currently Displayed]
  • In Silico development of CRISPR/Cas9 Construct for Oryza sativa subsp. indica. (deposited 15 Oct 2021 10:09)

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