Novelties in Gene Targeting in Plants

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (30 June 2023) | Viewed by 2802

Special Issue Editors


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Guest Editor
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
Interests: genomics; sequencing; gene; DNA sequencing; cloning; PCR

E-Mail Website
Guest Editor
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Prospekt Lavrentyeva 10, Russia
Interests: cytogenetic; QTL; novel gene targeting

Special Issue Information

Dear Colleagues,

Genome targeting (GT) has become the cutting-edge technology for genome reconstruction. Initially, it was based on homologous recombination (HR) that is able to precisely introduce desired modifications within a target locus. However, higher plants predominantly use non-homologous end joining (NHEJ), an error-prone DNA repair mechanism that tends to cause mutations which are not predictable on the sequence level. It was shown some time ago that site-specific nucleases are able to induce double-strand breaks at particular loci and stimulate both NHEJ and HR. Site-specific nucleases based on the CRISPR/Cas system are the most important development in recent biotechnology for genome engineering due to their ease in application. Many scientific works are devoted to the application of this approach in biotechnology and genome editing in order to improve such qualities as productivity, resistance to abiotic and biotic stresses, and nutritional properties for a number of agricultural plants such as rice, wheat, maize, etc. Despite all the advantages of CRISPR-Сas, there are also some limitations, in particular, a limited range of mutations, mainly genetic knockouts, low efficiency of delivery of vectors or RNP complexes to plant cells, and so on. However, many of these limitations we previously overcome successfully. This issue highlights recent progress in GT technologies in plants.

Dr. Andrey Borisovich Shcherban
Dr. Antonina Andreevna Kiseleva
Guest Editors

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Keywords

  • genome targeting
  • CRISPR/Cas
  • recombination
  • site-specific nucleases

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Published Papers (1 paper)

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13 pages, 2725 KiB  
Protocol
A Fast and Cost-Effective Genotyping Method for CRISPR-Cas9-Generated Mutant Rice Lines
by Abdugaffor Ablazov, Abrar Felemban, Justine Braguy, Hendrik N. J. Kuijer and Salim Al-Babili
Plants 2023, 12(11), 2189; https://doi.org/10.3390/plants12112189 - 31 May 2023
Viewed by 2523
Abstract
With increasing throughput in both the generation and phenotyping of mutant lines in plants, it is important to have an efficient and reliable genotyping method. Traditional workflows, still commonly used in many labs, have time-consuming and expensive steps, such as DNA purification, cloning [...] Read more.
With increasing throughput in both the generation and phenotyping of mutant lines in plants, it is important to have an efficient and reliable genotyping method. Traditional workflows, still commonly used in many labs, have time-consuming and expensive steps, such as DNA purification, cloning and growing E. coli cultures. We propose an alternative workflow where these steps are bypassed, using Phire polymerase on fresh plant tissue, and ExoProStar treatment as preparation for sequencing. We generated CRISPR-Cas9 mutants for ZAS (ZAXINONE SYNTHASE) in rice with two guide RNAs. Using both a traditional workflow and our proposed workflow, we genotyped nine T1 plants. To interpret the sequencing output, which is often complex in CRISPR-generated mutants, we used free online automatic analysis systems and compared the results. Our proposed workflow produces results of the same quality as the old workflow, but in 1 day instead of 3 days and about 35 times cheaper. This workflow also consists of fewer steps and reduces the risk of cross contamination and mistakes. Furthermore, the automated sequence analysis packages are mostly accurate and could easily be used for bulk analysis. Based on these advantages, we encourage academic and commercial labs conducting genotyping to consider switching over to our proposed workflow. Full article
(This article belongs to the Special Issue Novelties in Gene Targeting in Plants)
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