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      Genome editing in Sub-Saharan Africa: a game-changing strategy for climate change mitigation and sustainable agriculture

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          ABSTRACT

          Sub-Saharan Africa’s agricultural sector faces a multifaceted challenge due to climate change consisting of high temperatures, changing precipitation trends, alongside intensified pest and disease outbreaks. Conventional plant breeding methods have historically contributed to yield gains in Africa, and the intensifying demand for food security outpaces these improvements due to a confluence of factors, including rising urbanization, improved living standards, and population growth. To address escalating food demands amidst urbanization, rising living standards, and population growth, a paradigm shift toward more sustainable and innovative crop improvement strategies is imperative. Genome editing technologies offer a promising avenue for achieving sustained yield increases while bolstering resilience against escalating biotic and abiotic stresses associated with climate change. Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein (CRISPR/Cas) is unique due to its ubiquity, efficacy, alongside precision, making it a pivotal tool for Sub-Saharan African crop improvement. This review highlights the challenges and explores the prospect of gene editing to secure the region’s future foods.

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          Most cited references232

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          A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.

          Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems provide bacteria and archaea with adaptive immunity against viruses and plasmids by using CRISPR RNAs (crRNAs) to guide the silencing of invading nucleic acids. We show here that in a subset of these systems, the mature crRNA that is base-paired to trans-activating crRNA (tracrRNA) forms a two-RNA structure that directs the CRISPR-associated protein Cas9 to introduce double-stranded (ds) breaks in target DNA. At sites complementary to the crRNA-guide sequence, the Cas9 HNH nuclease domain cleaves the complementary strand, whereas the Cas9 RuvC-like domain cleaves the noncomplementary strand. The dual-tracrRNA:crRNA, when engineered as a single RNA chimera, also directs sequence-specific Cas9 dsDNA cleavage. Our study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing.
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            Multiplex genome engineering using CRISPR/Cas systems.

            Functional elucidation of causal genetic variants and elements requires precise genome editing technologies. The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage. We engineered two different type II CRISPR/Cas systems and demonstrate that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells. Cas9 can also be converted into a nicking enzyme to facilitate homology-directed repair with minimal mutagenic activity. Lastly, multiple guide sequences can be encoded into a single CRISPR array to enable simultaneous editing of several sites within the mammalian genome, demonstrating easy programmability and wide applicability of the RNA-guided nuclease technology.
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              Genome engineering using the CRISPR-Cas9 system.

              Targeted nucleases are powerful tools for mediating genome alteration with high precision. The RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system can be used to facilitate efficient genome engineering in eukaryotic cells by simply specifying a 20-nt targeting sequence within its guide RNA. Here we describe a set of tools for Cas9-mediated genome editing via nonhomologous end joining (NHEJ) or homology-directed repair (HDR) in mammalian cells, as well as generation of modified cell lines for downstream functional studies. To minimize off-target cleavage, we further describe a double-nicking strategy using the Cas9 nickase mutant with paired guide RNAs. This protocol provides experimentally derived guidelines for the selection of target sites, evaluation of cleavage efficiency and analysis of off-target activity. Beginning with target design, gene modifications can be achieved within as little as 1-2 weeks, and modified clonal cell lines can be derived within 2-3 weeks.
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                Author and article information

                Journal
                GM Crops Food
                GM Crops Food
                GM Crops & Food
                Taylor & Francis
                2164-5698
                2164-5701
                31 October 2024
                2024
                31 October 2024
                : 15
                : 1
                : 279-302
                Affiliations
                [a ]Plant Breeding Programme, Pan African University Life and Earth Sciences Institute (Including Health and Agriculture); , Ibadan, Nigeria
                [b ]Department of Irrigated Crop, National Agricultural Research Institute of Niger (INRAN); , Niamey, BP, Niger
                [c ]Department of Biological Sciences, Biotechnology Unit, Faculty of Science, Kings University; , Ode-Omu, Nigeria
                [d ]Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University; , Mmabatho, South Africa
                [e ]Department of Crop and Horticultural Science, Faculty of Agriculture, University of Ibadan; , Ibadan, Nigeria
                Author notes
                CONTACT Abdoul-Razak Oumarou Mahamane abdoulrazak1957@ 123456yahoo.com Plant Breeding Programme, Pan African University Life and Earth Sciences Institute (Including Health and Agriculture), Ibadan, Nigeria
                Omena Bernard Ojuederie ob.ojuederie@ 123456kingsuniversity.edu.ng Department of Biological Sciences, Biotechnology Unit, Faculty of Science, Kings University, Ode-Omu, Nigeria
                Author information
                https://orcid.org/0009-0005-0042-4326
                https://orcid.org/0000-0003-0474-6697
                Article
                2411767
                10.1080/21645698.2024.2411767
                11533803
                39481911
                24a31ee7-6b67-45e4-804c-8685644df13b
                © 2024 The Author(s). Published with license by Taylor & Francis Group, LLC.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The terms on which this article has been published allow the posting of the Accepted Manuscript in a repository by the author(s) or with their consent.

                History
                Page count
                Figures: 4, Tables: 2, References: 236, Pages: 24, Words: 8510
                Categories
                Review Article
                Review

                climate resilience,crispr/cas9,crop improvement,food security,gene editing,plant breeding,sustainable agriculture

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