Open Access

ARTICLE

In silico Prediction and Analysis of Potential Off-Targets and Off-Target Mutation Detection in StERF3-Gene Edited Potato Plants

by Hafiza Arooj Razzaq¹, Siddra Ijaz^1,*, Imran Ul Haq², Faisal Saeed Awan¹

1 Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, 38040, Pakistan
2 Department of Plant Pathology, University of Agriculture, Faisalabad, 38040, Pakistan

* Corresponding Author: Siddra Ijaz. Email:

(This article belongs to the Special Issue: Agricultural Intensification, Climate Change, and Food Security)

Phyton-International Journal of Experimental Botany 2023, 92(8), 2451-2460. https://doi.org/10.32604/phyton.2023.030501

Received 10 April 2023; Accepted 11 May 2023; Issue published 25 June 2023

Abstract

The imperative aspect of the CRISPR/Cas9 system is a short stretch of 20 nucleotides of gRNA that control the overall specificity. Due to the small size, the chance of its multiple occurrences in the genome increases; however, a few mismatches are tolerated by the Cas9 endonuclease activity. An accurate and careful in silico-based off-target prediction while target selection is preferred to address the issue. These predictions are based on a comprehensive set of selectable parameters. Therefore, we investigated the possible off-target prediction and their screening in StERF3 gene-edited potato plants while developing StERF3-loss-of-function mutants using CRISPR/Cas9 approach. The 201 off-targets for the selected targets of the StERF3 gene were predicted, and 79 were filtered as potential off-targets. Of these 79, twenty-five off-targets showed scores with defined cut-off values <0.5 and were analyzed in Sterf3-edited potato plants compared to wild-type plants. No off-targeting was found to have occurred in edited plants.

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Keywords

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Supplementary Material

Supplementary Material File

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