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Plant genome editing to achieve food and nutrient security


Genome editing enables precise genetic manipulation in plants, offering hope for tackling global food insecurity and malnutrition by enhancing crop traits and nutritional content. The BMC Methods Collection ‘Genome Editing in Plants’ will showcase advancements in the field, including target selection, delivery systems, off-target effects, and efficiency optimization.

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Genome editing is a versatile technology for precise manipulation of genetic material in different organisms, including plants. Originally, homologous recombination (HR) was employed for gene knockout, but its practical application was limited by low editing efficiency and labour-intensive procedures [1]. Following this, RNA-mediated interference (RNAi) was adopted for gene knockdown studies; however, it frequently resulted in incomplete and non-specific effects [2]. Subsequently, site-directed nucleases, including meganucleases (MNs), zinc finger nucleases (ZFNs), and transcription activator-like effector nucleases (TALENs), were introduced to enable targeted knockout or knockdown studies by inducing double-strand breaks (DSBs) at specific loci. However, these methods remain expensive and require extensive plasmid construction alongside labor-intensive protocols [3]. To address these limitations, the discovery of the CRISPR-Cas9 genome editing tool in 2012 emerged as a transformative breakthrough [4]. In this system, a single guide RNA (sgRNA) directs Cas9 to precisely target and cut the genome. Due to its simplicity, cost-effectiveness, and ease of use, the scientific community rapidly embraced the CRISPR/Cas9 system as a reliable and user-friendly tool for editing genomes across various organisms. While Cas9 remains the most widely used nuclease, alternative programmable Cas variants, including Cas12, Cas13 and Cas14 have been discovered to enhance the precision of CRISPR/Cas-mediated genome editing [3]. Following the developments of CRISPR/Cas9/12/13/14 tools, base editing was introduced in 2016, a CRISPR-Cas9-based genome editing technology that allows the introduction of point mutations in the DNA without generating DSBs. Two major classes of base editors have been developed: cytidine base editors or CBEs allowing C > T conversions and adenine base editors or ABEs allowing A > G conversions [5]. Finally, the ground-breaking prime editing system, introduced in 2019, represents a significant advancement in genome editing. Unlike conventional CRISPR methods, prime editing utilizes a longer guide RNA called pegRNA, along with a fusion protein comprising Cas9 H840 nickase and reverse transcriptase (RT). This innovative approach enables precise targeting of specific genomic loci minimizing off-target effects and offers the remarkable capability to delete or insert DNA sequences of substantial size, even up to kilobases, at predetermined locations in the genome [6].

Most of these tools have successfully been applied in diverse plants for various trait improvements during the past decade.

Application of genome editing in plants: prospects to achieve food and nutrient security

According to the Food and Agriculture Organization’s (FAO's) 2022 statistics, approximately 735 million people worldwide experience acute food shortages, and 3.1 billion people are unable to afford a healthy diet. Projections indicate that by 2030, nearly 600 million people will suffer from chronic undernourishment [7].

An effective strategy to address the challenges posed by a growing population and hunger is to enhance crop production and engage in agricultural activities in marginal areas. Over the past century, significant advancements in agricultural production and innovations have played a pivotal role in the success of the Green Revolution. During this period, efforts were focused on enhancing the genetic traits of traditional crops. These included selecting for higher yield potential, adaptability to diverse environments, shorter growth duration, improved grain quality, and resistance to biotic and abiotic stresses such as pests, diseases, drought, and flooding. As a result of these initiatives, cereal crop production tripled while the cultivated land area increased by only 30%. The Green Revolution led to significant reductions in poverty and food prices, underscoring its profound impact on global food security and socioeconomic well-being [8].

However, modern agricultural production faces unprecedented challenges such as global warming, rapidly changing climate conditions, soil salinization, and the accumulation of pollutants in the soil, resulting in toxic effects. These challenges require faster responses and more effective solutions that cannot be addressed by traditional agricultural methods [9].

Expanding upon the increasing availability of complete DNA sequences for numerous crops, genome editing technologies, especially CRISPR-Cas-mediated genome editing, provide a faster and more precise way to enhance crop improvement compared to traditional breeding methods [10].

Genome editing is now being applied to a wide range of crops in several countries, primarily focusing on enhancing crop yield and related traits such as tolerance to biotic and abiotic stresses. This aims to increase agricultural productivity, thus mitigating hunger, while also addressing nutritional deficiencies by enhancing the nutrient content of crops [11]. In rice, a staple for a large portion of the world's population, numerous genome editing studies target improving quality and resistance to diseases and pathogens [12, 13]. Similarly, genome editing efforts in wheat, another vital crop in human nutrition, aim to enhance its nutritional profile by modifying the levels of amylose and gliadin well [14]. Interestingly, genome edited crops such as waxy corn, anti-browning fungi, high-oleic soybeans, and γ-aminobutyric acid-rich tomatoes are already commercially available [15].

As genome editing technologies become more accessible and cost-effective, they hold significant promise for a wide array of benefits. For consumers, these advantages encompass improved nutrition, enhanced food safety, and reduced food waste. Farmers will benefit from increased resistance to diseases, weeds, and pests, as well as more affordable seeds due to lower production costs. Additionally, genome editing offers opportunities to bolster climate resilience and enhance biodiversity within cropping systems.

However, it is important to acknowledge the potential risks associated with genome edited crop varieties. These include non-target edits that may compromise safety or agronomic performance, as well as concerns regarding transparency, equity in technology spread and regulatory oversight. Therefore, it is crucial to consider scientific, political, and social factors when determining how to sustainably regulate and promote the safe use of genome-edited plants.

Acknowledging the importance of this field, we are pleased to announce that we are now accepting submissions to our Collection titled "Genome Editing in Plants." For more information, please visit: We believe that this collection will serve as a valuable platform for sharing novel protocols and methods to drive advancements in this area.

Availability of data and materials

No datasets were generated or analysed during the current study.



Homologous recombination


RNA-mediated interference


Double-strand break




Zinc finger nucleases


Transcription activator-like effector nucleases


Single guide RNA


Clustered Regularly Interspaced Short Palindromic Repeats


Cytidine base editors


Adenine base editors


Reverse transcriptase


Food and Agriculture Organization


  1. Capecchi MR. Altering the genome by homologous recombination. Science (80-). 1989;244(4910):1288–92.

    Article  CAS  Google Scholar 

  2. Krueger U, Bergauer T, Kaufmann B, Wolter I, Pilk S, Heider-Fabian M, et al. Insights into effective RNAi gained from large-scale siRNA validation screening. Oligonucleotides. 2007;17(2):237–50.

    Article  CAS  PubMed  Google Scholar 

  3. Hillary VE, Ceasar SA. A review on the mechanism and applications of CRISPR/Cas9/Cas12/Cas13/Cas14 proteins utilized for genome engineering. Mol Biotechnol. 2022.

  4. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science (80-). 2012;337(6096):816–21.

    Article  CAS  Google Scholar 

  5. Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature. 2016;533(7603):420–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Anzalone AV, Randolph PB, Davis JR, et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature. 2019;576:149–57.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. FAO, IFAD, UNICEF, WFP and WHO. 2023. The State of Food Security and nutrition in the World 2023. Urbanization, agrifood systems transformation and healthy diets across the rural–urban continuum. Rome: FAO

  8. Khush G. Green revolution: the way forward. Nat Rev Genet. 2001;2:815–22.

    Article  CAS  PubMed  Google Scholar 

  9. Gogolev YV, Ahmar S, Akpinar BA, Budak H, Kiryushkin AS, Gorshkov VY, Hensel G, Demchenko KN, Kovalchuk I, Mora-Poblete F, et al. OMICs, epigenetics, and genome editing techniques for food and nutritional security. Plants. 2021;10:1423.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Cardi T, Murovec J, Bakhsh A, Boniecka J, Bruegmann T, Bull SE, Eeckhaut T, Fladung M, Galovic V, Linkiewicz A, Lukan T, Mafra I, Michalski K, Kavas M, Nicolia A, et al. CRISPR/Cas-mediated plant genome editing: outstanding challenges a decade after implementation. Trends Plant Sci. 2023;28:1144–65.

    Article  CAS  PubMed  Google Scholar 

  11. Tiwari M, Kumar Trivedi P, Pandey A. Emerging tools and paradigm shift of gene editing in cereals, fruits, and horticultural crops for enhancing nutritional value and food security. Food Energy Secur. 2021;10:e258.

    Article  Google Scholar 

  12. Oliva R, Ji C, Atienza-Grande G, Huguet-Tapia JC, Perez-Quintero A, Li T, Eom JS, Li C, Nguyen H, Liu B, Auguy F, Sciallano C, Luu VT, Dossa GS, Cunnac S, Schmidt SM, Slamet-Loedin IH, Vera Cruz C, Szurek B, … Yang B. Broad-spectrum resistance to bacterial blight in rice using genome editing. Nature Biotechnol 2019;37(11):1344–1350.

  13. Dong OX, Yu S, Jain R, Zhang N, Duong PQ, Butler C, Li Y, Lipzen A, Martin JA, Barry KW, Schmutz J, Tian L, Ronald PC. Marker-free carotenoid-enriched rice generated through targeted gene insertion using CRISPR-Cas9. Nat Commun. 2020;11:1178.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Zhang S, Zhang R, Gao J, Song G, Li J, Li W, Qi Y, Li Y, Li G. CRISPR/Cas9-mediated genome editing for wheat grain quality improvement. Plant Biotechnol J. 2021;19(9):1684–6. Epub 2021 Jul 5. PMID: 34143557; PMCID: PMC8428824.

    Article  PubMed  PubMed Central  Google Scholar 

  15. Nagamine A, Ezura H. Genome editing for improving crop nutrition. Front Genome Ed. 2022;9(4):850104.

    Article  Google Scholar 

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The authors thank BMC Methods for the opportunity to be part of the journal and organise a special Collection on plant genome editing.


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SAC and MK conceived and drafted the Editorial. All authors read and approved the final manuscript.

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Correspondence to Stanislaus Antony Ceasar.

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Ceasar, S.A., Kavas, M. Plant genome editing to achieve food and nutrient security. BMC Methods 1, 3 (2024).

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