CRISPR-driven genome modification and biofortification: innovative techniques for creating climate-resistant and nutritionally improved crops

1 Introduction

The global agricultural sector is currently confronted with a multitude of challenges that jeopardize food security and human health on an unprecedented scale. With projections indicating that the world population will reach 9.7 billion by 2050, agricultural productivity must rise by 60-70% to satisfy increasing food demands (Hamad and Tayel, 2026). Moreover, climate change presents new stressors, such as higher temperatures, modified precipitation patterns, and a greater frequency of extreme weather events, which fundamentally change the environmental conditions under which crops have historically grown (Alotaibi, 2023).

In addition to quantity, the quality of produced food has become a significant issue. Micronutrient deficiencies, often referred to as “hidden hunger,” impact over 2 billion individuals worldwide, with deficiencies in iron, zinc, vitamin A, and folate being especially common in developing countries where staple crops are the main dietary source (Yilmaz and Yilmaz, 2025). Traditional methods of addressing these issues through conventional breeding and agronomic practices have been inadequate because of the time constraints and complexity of the desired traits.

Conventional breeding, while foundational to twentieth-century agricultural gains, faces intrinsic limitations in addressing these compounding pressures. Breeding cycles for many staple crops require 8–12 years to develop and release a new variety, a timeline poorly matched to the pace of climate change. Furthermore, many priority traits, such as combined abiotic stress tolerance and micronutrient density, are polygenic and are often linked to yield penalties or unfavorable agronomic traits when introgressed through wide crosses, limiting the effectiveness of marker-assisted selection alone (Gao et al., 2024; Kondwakwenda et al., 2021). These constraints have driven growing interest in precision genome-editing tools capable of introducing or stacking targeted changes without the linkage drag associated with conventional crossing.

Genome editing has moved from a laboratory technique to a field-deployed technology at considerable speed: more than 25 plant species have already been edited via CRISPR/Cas9, spanning more than 100 genes across major crop species for traits ranging from yield to stress tolerance to nutritional quality (Manghwar et al., 2020). Several of these edits have progressed beyond proof-of-concept into commercial or near-commercial release, including genome-edited rice varieties approved in India in 2025, underscoring that the translational gap between laboratory demonstration and field deployment, while still substantial, is beginning to close for a subset of traits and crops.

The emergence of precision genome editing technologies, particularly CRISPR/Cas9 systems, has transformed our ability to swiftly and accurately modify crop genomes to improve both their resilience and nutritional value (Angon et al., 2023; Jahan et al., 2025). Climate change threatens global crop yields and food security as a result of rising atmospheric temperatures, unpredictable rainfall, and elevated soil temperature and severe drought, making the development h. of climate-resilient varieties an urgent necessity. Moreover, biofortification strategies seek to increase the bioavailable levels of essential micronutrients in staple crops, providing a sustainable solution to combat malnutrition.

This review examines the present state and future potential of CRISPR-mediated genome editing and biofortification for crop improvement. Rather than proceeding crop-by-crop or gene-by-gene structure, the discussion is organized around a logical progression from trait class to molecular target, editing strategy, and agronomic outcome. The review first establishes the mechanistic foundations shared across all applications discussed thereafter. It then critically examines biofortification, climate resilience, and disease and/or pest resistance in turn, each identifying the molecular targets and editing strategies used and, where reported, the validation stage of the resulting phenotype. Finally, the review evaluates the technical, regulatory, and governance constraints that determine whether these interventions can move from proof-of-concept to field deployment.

2 CRISPR/Cas9 technology in crop improvement

2.1 Mechanistic foundations and technical advances

The CRISPR/Cas9 system, initially identified as an adaptive immune response in prokaryotes, has been effectively repurposed for accurate genome editing in eukaryotic organisms, such as crop plants (Arora and Narula, 2017). This technology comprises two primary elements: a guide RNA (gRNA) that identifies the target DNA sequence and the Cas9 endonuclease that creates double-strand breaks at designated locations (Aljabali et al., 2024). CRISPR technology serves as a robust instrument that enables researchers to more readily modify DNA sequences and alter gene function in both animals and plants (Chen et al., 2024; Chehelgerdi et al., 2024).

Recent advancements in technology have markedly improved the precision and efficiency of CRISPR applications in agricultural crops (Chen et al., 2024). The emergence of high-fidelity Cas9 variants, such as SpCas9-HF1 and eSpCas9, has minimized off-target effects while preserving on-target efficiency (Tsai et al., 2016). Base editing technologies, which employ cytosine and adenine base editors, facilitate accurate single nucleotide alterations without causing double-strand breaks, thereby broadening the options for subtle genetic modifications (Yang X. et al., 2024).

Prime editing signifies another notable progress, enabling targeted insertions, deletions, and replacements with minimal off-target effects (Figure 1). This technology has demonstrated particular utility in introducing advantageous alleles from wild relatives or in creating novel regulatory sequences to influence gene expression patterns (Lu et al., 2024).

2.2 Applications in major crop species

2.2.1 Cereal crops

Rice, wheat, and maize are the three most essential cereal crops worldwide, accounting for approximately 60% of caloric intake for humans (Palacios-Rojas et al., 2020). The application of CRISPR technology in these crops has been aimed primarily at improving yield, stress resilience, and nutritional value (Basu et al., 2023).

In the case of rice, successful CRISPR modifications have been accomplished for various traits at once (Shaheen et al., 2023). The alteration of the OsERF109 gene has led to improved drought resistance while ensuring yield stability during water scarcity (Parmar et al., 2025). Similarly, changes in the OsNAC family of transcription factors have resulted in increased drought and salt tolerance, with field trials indicating a 15–20% increase in yield under stress conditions compared with traditional varieties (Jeong et al., 2010).

Editing the wheat genome has been more complex because of its hexaploid structure, necessitating the simultaneous editing of homeologous genes across three subgenomes. Nevertheless, recent achievements include the creation of wheat varieties that exhibit greater resistance to powdery mildew through the targeted disruption of MLO genes, as well as improved protein quality via modifications to gluten composition (Roychowdhury et al., 2024).

In maize, the focus has been predominantly on enhancing herbicide tolerance and insect resistance. The creation of CRISPR-edited maize that shows increased resistance to fall armyworm through the modification of protease inhibitor genes represents a significant step forward in sustainable pest management (Kumari et al., 2024).

2.2.2 Legume crops

Owing to their ability to fix nitrogen biologically, legumes are essential for human nutrition and agricultural sustainability. The application of CRISPR technology in legumes has aimed at increasing nitrogen fixation efficiency, improving protein quality, and increasing stress tolerance.

In the case of soybean, the editing of GmFT family genes has led to the development of varieties with better control over flowering time, which facilitates cultivation across various climatic zones (Yuan et al., 2022). Furthermore, alterations in fatty acid desaturase genes have resulted in oils with superior nutritional profiles, notably those with higher omega-3 fatty acid contents (Pham et al., 2011).

The enhancement of cowpea and common bean through CRISPR has focused on improving drought tolerance and protein digestibility (Jha et al., 2022). The modification of genes associated with antinutrient production has yielded varieties with lower levels of phytic acid and tannins, thereby increasing the bioavailability of protein and minerals (Raizada et al., 2023).

2.3 Multiplexed genome editing for complex traits

The advancement of multiplexed CRISPR systems has made it feasible to edit several genes at once, thereby aiding in the enhancement of intricate, polygenic traits. Recent progress in the design and delivery of guide RNAs has enabled the simultaneous editing of 5–10 target sites with remarkable efficiency (Cheng et al., 2025).

Multiplexed strategies have been shown to be especially beneficial for improving disease resistance by targeting various susceptibility genes or establishing durable resistance through gene pyramiding (Latif et al., 2025). The concurrent disruption of multiple SWEET genes in rice has led to broad-spectrum resistance against bacterial blight while preserving normal plant growth (Zhang et al., 2024).

2.4 Commercial and field-released case studies

Recent examples show that a small but growing set of genome-edited crop traits has moved beyond greenhouse validation into field evaluation or market introduction. In India, a recent report on KAMALA describes a CRISPR/Cas12a-edited Samba Mahsuri derivative at CKX2/Gn1a that showed superior agronomic performance in 18 field locations, with an average 19% grain-yield increase, earlier maturity, and intact grain quality; the same report states that KAMALA was registered as the first genome-edited variety ready for cultivation by Indian farmers (Solanki et al., 2026). In Japan, the Sicilian Rouge high-GABA tomato was notified to the government as the first gene-edited tomato, seedling distribution began in 2021, and online fruit sales followed later that year. Other translational examples include high-oleic soybean, where TALEN-mediated disruption of FAD2-1A/FAD2-1B increased seed oleic acid from 20% to 80% and CRISPR/Cas9 editing raised it from 11% to as much as 85% in double mutants (Haun et al., 2014; Fu et al., 2022). Camelina provides a parallel oil-quality example: CRISPR/Cas9 editing increased oleic acid from 16% to over 50% and produced oils described as better suited for production of commercial chemicals, including biofuels (Jiang et al., 2017). Table 1 summarizes these cases alongside their validation stage and regulatory basis.

Table 1. Commercial and field-validated CRISPR-edited crop releases.

3 Biofortification strategies and genomic approaches

3.1 Conventional vs. genetic biofortification

Biofortification is a promising approach for increasing the levels of essential nutrients such as iron, zinc, iodine, and vitamin A in the consumable parts of various crop plants (Avnee et al., 2023). Crop biofortification can be achieved through either agronomic practices or genetic breeding methods. While agronomic biofortification, achieved through the application of fertilizers, offers immediate yet temporary results, genetic biofortification provides sustainable, long-lasting enhancements that are passed down to future generations (Bhardwaj et al., 2022; Naik et al., 2024).

Genetic biofortification techniques include both traditional breeding methods that utilize natural genetic diversity and transgenic approaches that introduce new biosynthetic pathways (Wang and Liu, 2025). The use of genomic tools, such as marker-assisted selection (MAS) and genomic selection (GS), has greatly accelerated the process of identifying and incorporating beneficial alleles that improve micronutrient content (Kumar et al., 2024).

3.2 Micronutrient enhancement pathways

3.2.1 Iron and zinc biofortification

Iron and zinc deficiencies impact more than 1.6 billion individuals worldwide, with pregnant women and children being especially at risk (Gregory et al., 2017). Genetic strategies aimed at increasing iron and zinc levels have focused on three main approaches: increasing absorption from the soil, improving transport within the plant, and increasing storage in consumable tissues (Hamzah Saleem et al., 2022).

The overexpression of nicotianamine synthase (NAS) genes has been shown to be effective across various crop species (Zha et al., 2022; Wang M. et al., 2013). In rice, transgenic lines that express barley NAS genes present 2–4-fold increases in iron and zinc levels in polished grains, along with improved bioavailability in human cell culture tests (Masuda et al., 2008; Zha et al., 2022; Wang M. et al., 2013). Comparable methods applied to wheat have produced varieties with a 40–60% increase in grain zinc content while preserving agronomic performance (Ram et al., 2024).

Another effective strategy is the overexpression of the iron storage protein ferritin. The incorporation of soybean ferritin genes into rice has led to increases of up to 6 times in iron content, with field trials verifying their stability across various environments (Goto et al., 1999). The integration of enhanced uptake, transport, and storage has resulted in synergistic effects, with certain varieties reaching iron levels adequate to fulfill 50–70% of daily requirements through regular consumption.

3.2.2 Vitamin A enhancement

Vitamin A deficiency affects approximately 250 million children worldwide and is a primary cause of preventable blindness (Mejia and Erdman, 2025). The creation of golden rice, which is fortified with β-carotene (provitamin A), has led the way in genetic biofortification methods and has shown potential for integrating complex biosynthetic pathways into staple crop species.

Recent developments have concentrated on enhancing carotenoid biosynthesis via metabolic engineering. The synchronized expression of the genes encoding phytoene synthase, phytoene desaturase, and lycopene β-cyclase has been optimized to reach β-carotene concentrations of 20–30 μg/g in rice endosperm, which is adequate for fulfilling 50–60% of the daily vitamin A needs (Tian et al., 2019). Comparable strategies involving cassava, an essential staple in sub-Saharan Africa, have produced varieties with increased β-carotene levels while preserving the natural drought resistance of these crops (Ceballos et al., 2012).

The enhancement of carotenoid stability during storage and processing continues to be a significant challenge. Recent studies have pinpointed genes associated with carotenoid degradation, and their precise modification has led to better retention of provitamin A levels during postharvest management (Gebregziabher et al., 2023).

3.2.3 Protein quality enhancement

In addition to micronutrients, protein is a vital nutritional element, especially in areas where plant proteins are the main source of protein. Deficiencies in essential amino acids, particularly lysine and methionine, are prevalent in diets that are primarily based on cereals.

CRISPR-mediated techniques have effectively improved protein quality across various crop species. In maize, the alteration of zein genes, along with the overexpression of proteins rich in lysine, has led to varieties that present a 40–50% increase in lysine content (Wang et al., 2025). Similarly, changes in rice prolamin genes have enhanced both protein digestibility and the profiles of essential amino acids (Jukanti et al., 2025).

The creation of crops with improved protein content and quality through biofortification methods has demonstrated significant potential in combating protein-energy malnutrition among at-risk populations. Recent progress in the understanding of protein storage mechanisms has facilitated more precise strategies for simultaneously enhancing both the quantity and quality of proteins.

3.2.4 Folate and B-vitamin biofortification

Folate (vitamin B9) deficiency, identified in the introduction as a major component of hidden hunger, has received less genome-editing attention than iron, zinc, or vitamin A, but it fits the same metabolic-engineering logic. In plants, folate biosynthesis runs through the pterin and para-aminobenzoate branches, and transgenic work in tomato and rice showed that boosting the two rate limiting enzymes, GTP cyclohydrolase I and aminodeoxychorismate synthase, can raise folate content several-fold, in some cases much more (Garza et al., 2007; Dong et al., 2014). CRISPR-based folate biofortification is still at an earlier stage: recent reviews describe only a few folate-oriented CRISPR strategies, mainly promoter tuning, base editing, or enhancer reconfiguration at regulatory loci rather than coding-sequence knockouts. That makes the folate section a real gap relative to the broader CRISPR biofortification literature, not an oversight (Khan et al., 2024).

3.3 CRISPR-specific versus conventional transgenic biofortification

Much of the biofortification literature in Sections 3.2.1–3.2.3, including the iron- and zinc-enhancing NAS/ferritin work and Golden Rice, was built on conventional transgenic overexpression rather than CRISPR editing: one rice study constitutively overexpressed OsNAS1, OsNAS2, or OsNAS3, another combined dicot ferritins with OsNAS2, and Golden Rice was created by introducing carotenoid-pathway cDNAs into rice endosperm by genetic engineering (Johnson et al., 2011; Beyer et al., 2002). By contrast, CRISPR biofortification more often targets endogenous loci, including negative regulators and native regulatory elements; recent reviews explicitly frame CRISPR-Cas9 gene knockout targets and promoter/cis-element editing as routes to improving mineral accumulation (Yadav et al., 2023). The CRISPR-edited Sicilian Rouge GABA tomato illustrates the shift: CRISPR/Cas9 deleted the autoinhibitory domain of SlGAD2 and SlGAD3, and Japan clarified its genome-editing regulatory pathway in 2019, a framework that many reviews describe as less restrictive than transgenic regulation (Nonaka et al., 2017). That regulatory asymmetry may help explain why knockout or regulatory-editing strategies could become more common in CRISPR biofortification than the overexpression strategy that dominated the transgenic literature (Matsuo and Tachikawa, 2022; Labuschagne, 2023).

4 Climate resilience through CRISPR

4.1 Shared molecular architecture of abiotic stress signaling

Before considering drought, heat, and salinity tolerance individually, it is useful to recognize that these three stresses converge on a largely overlapping molecular signaling core, and that CRISPR-based interventions in this core frequently have consequences across more than one stress category. Three interconnected nodes recur throughout the literature discussed below (Table 2).

Table 2. Core molecular signaling nodes shared across drought, heat, and salinity responses.

The first is the abscisic acid (ABA)–SnRK2–AREB/ABF axis. ABA is the central hormone coordinating stomatal closure and stress-responsive gene expression under both water deficit and osmotic stress; within this network, AREB/ABF transcription factors and SnRK2 kinases act as the principal regulators (Margay et al., 2024). AREB1 in particular governs osmotic stress signaling, antioxidant defense, and ABA biosynthesis, and its inactivation increases drought susceptibility while its overexpression enhances tolerance (Yoshida et al., 2015; Fujita et al., 2005). CRISPR/Cas9-based epigenetic editing that increased AREB1 promoter acetylation in Arabidopsis elevated AREB1 transcription and improved survival, stomatal regulation, and chlorophyll retention under drought (Paes de Melo et al., 2020). AtSnRK2.8 similarly activates drought-responsive genes through the AREB–ABF axis, and SnRK2 subclasses in rice enhance growth and stress adaptation more broadly (Amjad et al., 2024).

The second node is the Ca²⁺–CDPK–MAPK–HSF cascade. Heat stress triggers rapid Ca²⁺ influx through membrane calcium channels; the resulting Ca²⁺ signal is decoded by calcium-binding proteins, calmodulins, and calcium-dependent protein kinases (CDPKs), and propagated through mitogen-activated protein kinases (MAPKs) and phosphatases (Xu et al., 2022; Kumar et al., 2020). Successive phosphorylation/dephosphorylation cycles in this cascade activate heat shock transcription factors (HSFs), which in turn control membrane lipid saturation and the expression of protective heat shock proteins (Mizoi et al., 2019; Prasertthai et al., 2022). This same MAPK machinery is not heat-specific: SlMAPK3 in tomato, for example, regulates HSF/HSP activity under heat stress but also modulates drought-response phenotypes when disrupted, illustrating the cross-talk between the two nodes described here (Yu et al., 2019; Wang et al., 2017).

The third downstream node involves reactive oxygen species (ROS) accumulation and scavenging. Elevated ROS is a common consequence of drought, heat, and salinity stress, and rapid Ca²⁺ influx induces antioxidant systems, including ascorbate peroxidase (APX), superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPX), and related detoxification pathways, which help buffer oxidative damage across all three stress types (Hassan et al., 2021).

Because these nodes are shared rather than stress-specific, CRISPR edits targeting one of them, such as promoter-level ABA pathway modifications or MAPK knockouts, can produce pleiotropic effects across multiple stress categories. This pattern recurs in the trait-specific findings below. The following subsections therefore examine drought, heat, and salinity tolerance separately, organized by molecular target, CRISPR editing strategy, and reported outcome, rather than revisiting the shared signaling framework in each section.

4.2 Drought tolerance enhancement

Drought is a major constraint on crop productivity, disrupting photosynthesis, respiration, osmotic balance, and nutrient uptake (Zahra et al., 2023; Murad et al., 2024; Farooq et al., 2012). Because drought tolerance is polygenic, conventional breeding progress has been slow (Gao et al., 2024; Kondwakwenda et al., 2021), and CRISPR/Cas9 editing offers a more direct route to manipulating the ABA–SnRK2–AREB axis described in Section 4.1, alongside structural traits governing water use efficiency (Younas et al., 2024; Khaliq et al., 2024; Rai et al., 2023; Pandita, 2022).

Beyond the AREB1 epigenetic editing example already discussed in 4.1, CRISPR-based drought engineering has targeted structural and root-architecture traits: DRO1 modification promotes deeper rooting in rice, and analogous edits in maize and wheat enhance lateral root and xylem regulation to improve water uptake under limited rainfall (Jangir et al., 2023). Editing of wax biosynthesis genes thickens the cuticle and reduces water loss (Giri et al., 2021); the OST2/AHA1 mutation in Arabidopsis promotes favorable stomatal responses without evident fitness cost (Merlot et al., 2007); and editing of aquaporin regulatory regions improves root hydraulic conductivity (Chaumont and Tyerman, 2014). Table 3 summarizes the principal gene-level interventions reported across species.

Table 3. CRISPR-based interventions for drought tolerance across crop species.

Because drought tolerance is polygenic, single-gene edits typically yield incremental gains; multiplex editing that simultaneously targets ABA regulators, ROS-scavenging enzymes, and osmolyte biosynthesis genes has produced larger improvements (Jangir et al., 2023), and base and prime editing now allow narrower, more specific allelic variants that reduce the yield trade-offs historically associated with drought-tolerance loci (Karunarathne et al., 2023). Notably, most of the gene-level findings in Table 3 have been validated only in controlled greenhouse or growth-chamber conditions; the ARGOS8 maize result is a rare example of field-level validation, underscoring a broader translational gap discussed further in Section 6.

4.3 Heat stress tolerance

Heat stress, defined here as exposure to temperatures 10–15 °C above a crop’s threshold, disrupts protein and membrane stability and impairs photosynthesis by reducing chlorophyll content and inhibiting photosystem II and RuBisCO activity (Choudry et al., 2024; Roy and Shil, 2020). Its most important yield impact is on reproduction: reduced pollen viability, premature anthesis, and defective pollen development are major drivers of heat-induced yield loss in cereals and legumes (Hassan et al., 2021). The Ca²⁺–CDPK–MAPK–HSF signaling cascade, together with ROS-scavenging systems, mediates the heat-response network described in Section 4.1, and crop performance under heat stress is closely associated with preservation of photosynthetic capacity, membrane integrity, and water-use efficiency (Gan and Ling, 2022).

CRISPR/Cas9 editing has been applied to modify heat-sensitive genes across this framework (Table 4). In rice, triple-knockout of the ABA receptor genes OsPYL1/4/6 improved growth and grain yield under field heat stress, with taller plants, greater fresh weight, and more vigorous growth than wild type, providing a clear example of an ABA-pathway edit conferring heat tolerance (Miao et al., 2018). In tomato, SlMAPK3 knockout enhanced heat tolerance by modulating HSF/HSP activity (Yu et al., 2019), while disruption of the MADS-box gene SlAGL6 induced facultative parthenocarpy and reduced heat-associated losses in yield and pollen viability. In lettuce, reduced expression of LsNCED4 improved seed germination under heat stress, and in maize, mutation of the temperature-responsive male-sterility gene ZmTMS5 extended the fertile temperature range from 24–28 °C (Choudry et al., 2024).

Table 4. Modification of heat stress-responsive genes and their outcomes via CRISPR/Cas9.

4.4 Salinity tolerance

Salinity constrains growth through a combination of osmotic and ionotoxic stress: sodium accumulation in the soil first limits water uptake, then progressively accumulates in shoot tissues, where it disrupts photosynthesis and other physiological processes (Sheng et al., 2023; Munns and Tester, 2008; Van Zelm et al., 2020). This is an increasingly important constraint in coastal agricultural regions such as Bangladesh, where salinity-driven yield losses are already affecting farming livelihoods (Chen and Mueller, 2018). As with drought and heat, the ABA signaling axis and ROS-scavenging nodes described in Section 4.1 are central to the salinity response; the salinity-related CRISPR targets identified to date are summarized in Table 5.

Table 5. CRISPR-based interventions for salinity tolerance across crop species.

In maize, salt tolerance has so far been studied more through GWAS and QTL mapping than through direct CRISPR editing, although these approaches are increasingly being linked to genome editing to translate candidate loci into engineered tolerance (He et al., 2025). As Table 5 shows, salinity-tolerance edits converge largely on the same ABA-signaling and ROS-scavenging nodes highlighted in Section 4.1, rather than defining a separate mechanistic class. This pattern supports the view that drought, heat, and salinity tolerance in CRISPR-edited crops are better understood as trait-specific expressions of a shared regulatory network than as independent engineering problems.

5 Disease and pest resistance through CRISPR

5.1 Pathogen resistance strategies

Across the bacterial, fungal, oomycete, and viral pathogens discussed below, one strategy recurs more often than any other: knockout of a plant susceptibility (S) gene whose normal function pathogens exploit for colonization, rather than introduction of a novel resistance (R) gene. S genes such as the SWEET sugar transporters, MLO powdery-mildew susceptibility loci, and eIF4E/eIF4G viral translation factors are each hijacked by a different pathogen class through a different molecular mechanism, but the editing logic is the same in every case: removing the host factor removes the pathogen’s point of entry, typically without the yield or fitness cost associated with constitutively active R-gene-mediated defense. The subsections below are organized by pathogen type because the specific S genes and delivery contexts differ, but this S-gene-knockout logic — rather than the pathogen biology itself — is the unifying editing strategy connecting them.

Genome editing technologies are becoming the most popular and widely used genetic tools for identifying pathogen resistance. By enabling precise and targeted genome modifications, plant biology has been revolutionized. In particular, CRISPR-driven genome editing technologies play a pivotal role in the development of disease resistance in bacteria, fungi, viruses, and other pathogens. We are now discussing some disease strategies achieved by the CRISPR system in different pathogens.

5.1.1 Genome editing for resistance against bacterial pathogens

Bacterial infections are very diverse, multiply quickly, and can spread in a variety of ways, which makes them extremely difficult to control, particularly after outbreaks have started. Recent advances in understanding host–pathogen interactions have led to the identification of several host genes, including the susceptibility (S) gene, involved in these processes. Since loss of S gene function often provides durable resistance, these genes are key targets for genome editing in the breeding of bacterial disease-resistant crops (Yin and Qiu, 2019).

Using CRISPR/Cas technology to edit S genes can reduce a plant’s susceptibility to bacterial infections without affecting its growth or production. Since S genes encode proteins necessary for bacterial colonization and disease development, they are crucial to the plant–microbe relationship. Sugar transporters, for example, those that are crucial for bacterial pathogenicity, are encoded by the SWEET gene family. Similarly, the LOB1 gene is necessary for Xanthomonas to cause disease in some crops and is involved in regulating plant immunity (Zaidi et al., 2018). This strategy has already been effectively shown in a number of crops, such as rice, tomatoes, and citrus. The target gene’s DNA sequence is altered in specific ways to use CRISPR/Cas editing. With the use of a programmable RNA molecule, this method directs a nuclease enzyme to the precise location in the genome where it causes a double-strand break (Kim et al., 2019). The break is then repaired by the cell’s repair mechanisms, which may remove or add new DNA bases, changing the gene sequence. One way to decrease plant vulnerability to Xanthomonas and other bacterial infections is to target and alter particular genes that are necessary for bacterial colonization and disease development. This method may reduce the need for agrochemicals and provide farmers with more efficient and sustainable disease management techniques (Xu et al., 2019).

Therefore, the CRISPR/Cas system targets negative regulators of innate immunity and S genes to increase plant tolerance to microorganisms (Zaidi et al., 2018). For example, knocking down the TALE-targeted Os8N3 or OsSWEET11 gene in rice can provide resistance against Xanthomonas oryzae pv. oryzae (Xoo) (Kim et al., 2019). By focusing on the TALE-binding elements (EBEs) found in the promoter sequences of the “OsSWEET11” and “OsSWEET14” genes, strong resistance against numerous Xoo strains can be provided (Xu et al., 2019). In addition, the CRISPR/Cas system targeting the OsSWEET11/OsSWEET13/OsSWEET14 promoter sequence has resulted in broad-spectrum resistance (Oliva et al., 2019).

Tomatoes are among the most economically significant crops in the world, but their production and quality are still restricted by a number of serious diseases, such as Phytophthora spp., Xanthomonas spp., and Pseudomonas syringae (Schwartz et al., 2015). One gene, DMR6 (downy mildew resistance 6), was found to be mutated in Arabidopsis, resulting in elevated salicylic acid levels and resistance to a number of plant diseases, including bacteria and oomycetes, according to a recent study (Zeilmaker et al., 2015). Interestingly, P. syringae pv. Similarly, tomato and Phytophthora capsici infection causes an upregulation of the tomato ortholog SlDMR6-1. The CRISPR/Cas9 method produces null mutants of SlDMR6–1 that are resistant to P. syringae, P. capsici, and Xanthomonas without negatively impacting tomato growth and development (Thomazella et al., 2016). All of these findings point to the possibility that DMR6 knockout is an effective strategy for generating broad-spectrum disease resistance in plants (Yin and Qiu, 2019). The CRISPR/Cas12 and CRISPR/SpCas9 tools have also been demonstrated to be effective in producing resistance to citrus canker (Peng et al., 2017). Thus, CRISPR enables precise modification of susceptibility and resistance genes by offering sustainable solutions against bacterial pathogens.

5.1.2 Genome editing for resistance against fungal pathogens

Fungal pathogens have a major influence on agriculture and are the most prevalent cause of plant diseases. Owing to their diverse lives and high genetic flexibility, fungi can evolve resistance to fungicides, adapt to new hosts, and overcome resistance (R) gene-mediated resistance, making disease control difficult (Borrelli et al., 2018; Yin and Qiu, 2019).

Targeted mutagenesis has been effectively and accurately facilitated in plants by the CRISPR/Cas9 system to increase resistance to fungal infections. Mildew resistance locus O (MLO), a susceptibility gene, is the most extensively researched gene for fungal disease resistance (Jørgensen, 1992). Across monocots and dicots, the MLO gene is conserved and encodes an integral membrane protein with seven transmembrane domains (Acevedo-Garcia et al., 2014; Nekrasov et al., 2017). The tomato plants included 16 MLO genes, with SlMlo1 being a key gene influencing plant susceptibility to powdery mildew disease. It has been possible to knock out SlMlo1 in tomato plants via CRISPR/Cas9 technology. Without producing any additional undesirable phenotypic effects, the knockout mutants provided resistance to the powdery mildew fungus Oidium neolycopersici. By selfing first-generation (F0) resistant mutants, CRISPR/Cas9-mediated DNA transfer was eliminated through segregation, resulting in the production of second-generation progeny (F1). Resistance to O. neolycopersici was also demonstrated by the F1 offspring. CRISPR/Cas9 technology has also caused a mutation in the susceptibility gene Powdery Mildew Resistance 4 (PMR4), which is a callose synthase, and has given tomatoes resistance to O. neolycopersici (Santillán Martínez et al., 2020). Similarly, three copies of the TaEDR gene were knocked out immediately in wheat to confer resistance against powdery mildew (Zhang et al., 2017).

Rice blast resistance can be established via the use of CRISPR/Cas9 technology to interrupt the OsSEC3A gene, which codes for a subunit of the exocyst complex and specifically targets multiple sites, including the third and tenth exons of this gene. This mutation results in a lesion-mimic phenotype and dwarfism, but it also allows defense-responsive genes such as those encoding salicylic acid and PR proteins to be upregulated, increasing resistance to the blast pathogen (Ma et al., 2018). The same technique is used to modify the resistance gene Pi21, which codes for a cytoplasmic proline-rich protein that acts as a susceptibility factor (Fukuoka et al., 2009). Using CRISPR/Cas9 technology, Pi21 deletion increases rice resistance to blast pathogens without changing primary agronomic characteristics (Nawaz et al., 2020).

The BSR-D1 gene, another susceptibility factor, was deliberately mutated via CRISPR/Cas9 to increase blast resistance in rice. A single nucleotide alteration increases the binding of the MYBS1 TF, which inhibits peroxidase expression to increase hydrogen peroxide generation. Similarly, a novel rice peroxidase-producing gene (Perox3) was knocked out via CRISPR/Cas9 technology to assess its functional significance in resistance to blast disease (Zhu et al., 2020).

Additionally, in CRISPR/Cas9-modified wheat plants, one (TaMLO-A1) of the three MLO homoalleles enhanced resistance to infection by Blumeria graminis f. sp. tritici (Wang et al., 2014). It has been demonstrated that it is molecularly possible to remove VvMLO7 when CRISPR/Cas9 RNP is given to grapevine protoplasts; however, no plants have regenerated (Malnoy et al., 2016). Parallel experiments on RNAi plants revealed that when VvMLO7 was absent, grapevines were less vulnerable to Erysiphe necator (Pessina et al., 2016).

This is the overall scenario of CRISPR-driven strategies to increase host immunity and disrupt fungal infection pathways for durable resistance.

5.1.3 Disease resistance in oomycetes

Oomycetes are fungus-like microorganisms that play important roles in agriculture, aquaculture, forests, and natural ecosystems (Salmaninezhad et al., 2024). The top ten oomycete infections included seven species of Phytophthora, followed by Pythium, Hyaloperonospora, and Albugo. The three most dangerous oomycetes are Peronospora, Phytophthora, and Pythium (Kamoun et al., 2015).

Oomycete diseases can be decreased with the help of CRISPR/Cas technologies. According to (Lu et al. (2020), The resistance of A. thaliana to Phytophthora parasitica, a model organism of Phytophthora species, was enhanced when the PAMP-triggered immunity repressor AtERF019 (ethylene-responsive factor 19 gene) was knocked out via CRISPR/Cas9. Although sweet basil (Ocimum basilicum) ObDMR1 knockout mutants were produced, no pathogenicity testing was performed on these mutants (Navet and Tian, 2020). To introduce CRISPR/Cas9 components that target nonexpressor pathogenesis-related 3 (TcNPR3), a suppressor of the defensive response, into cacao leaves and cotyledon cells, genome editing was carried out in the cacao tree (Theobroma cacao) via Agrobacterium-mediated temporary transformation. The leaves whose TcNPR3 was removed presented increased resistance to black pod disease caused by Phytophthora tropicalis and upregulated the expression of defense genes, including pathogenesis-related (PR) genes (Zhao et al., 2018).

Another noteworthy accomplishment in this field is the creation of a multiplex CRISPR/Cas12a editing procedure for P. palmivora, which enables the simultaneous knockout of many genes. To increase the activity of the Cas12a enzyme at 25 °C, this strategy uses a time-efficient transformation technique that involves zoospore electroporation and a D156R point mutation. By effectively deleting the genes that encode adenine phosphoribosyltransferase (APT), this method has been utilized to produce mutants that are resistant to 2-fluoroadenine (2-FA) but still have full virulence against Nicotiana benthamiana (Verhoeven et al., 2024). As a functional substitute for antibiotic selection, 2-FA serves as a counterselection marker, providing greater adaptability for subsequent genetic modifications. Additionally, because base editors do not rely on DSBs, which can set off error-prone repair mechanisms, they have been demonstrated to minimize off-target effects in comparison with conventional CRISPR systems (Yang P. et al., 2024).

These developments in CRISPR/Cas12a technology not only expand the genetic arsenal that oomycetes can use but also make it easier to investigate the pathogenicity and function of genes. By making genome editing accurate and effective, scientists may create disease control plans and acquire a deeper understanding of the molecular underpinnings behind oomycete pathogenicity. The study of complicated traits regulated by numerous genes is made possible by the capacity to undertake multiplex gene editing, which speeds up research in this area (Vink et al., 2023).

5.1.4 Disease resistance to viruses

Plant viral infections are difficult to manage because of the rapid development of viruses and the frequent involvement of insect vectors. Over the past three decades, the widespread use of the transgenic synthesis of virus proteins or RNAs has improved plant viral resistance, a phenomenon known as pathogen-derived resistance (Ding and Vionnet, 2007). The majority of plant viruses have RNA genomes. The creation of new CRISPR/Cas systems, especially those that target RNA, offers new possibilities for developing RNA virus-resistant plants (Price et al., 2015).

Resistance to viruses can be attained by either modifying the host elements that promote the replication of viral species or by selectively identifying and eliminating distinct viral genomes to stop their replication (Ali et al., 2015). The cap-binding protein, often referred to as eukaryotic initiation factor 4E (eIF4E), is a key element in enhancing plant virus susceptibility (German-Retana et al., 2008). eIF4E inactivation produces innate immunity against potyviruses, which are members of the Potyviridae virus family, in a variety of plant species. A study revealed that cucumber plants transformed with eIF4E via CRISPR/SpCas9 exhibited resistance to several viruses, such as papaya ringspot mosaic virus-W (PRSMV-W), zucchini yellow mosaic virus (ZYMV), and cucumber vein yellowing virus (CVYV) (Gosavi et al., 2020).

A. thaliana and cassava eIF4E mutagenesis mediated by CRISPR/SpCas9 reduced the symptoms of turnip mosaic virus (TuMV) infection and cassava brown streak disease (Cao et al., 2020; Juma et al., 2022). By using the CRISPR/SpCas9 method to target eIF4G for mutation, tolerance against rice tungro spherical virus (RTSV) was discovered. In A. thaliana, resistance to clover yellow vein virus is achieved via cytidine base editing, which involves C > G conversion at N176K in eIF4E1 (wild type) (Bastet et al., 2019; Gomez et al., 2019).

Economically valuable crops such as pepper, tomato, and sugar beet can suffer significant damage from DNA viruses known as geminiviruses, which have a single-stranded circular genome. Using CRISPR/SpCas9, several investigations have directly targeted the genome of geminivirus (Beam and Ascencio-Ibáñez, 2020). Both the beet severe curly top virus (BSCTV) and the bean yellow dwarf virus (BeYDV) were targeted for their genomes via the CRISPR/SpCas9 system, which targets the intergenic region and replication-associated protein (Rep protein) (Cao et al., 2020; Khatodia et al., 2017). Following modification, the viruses became A. thaliana and N. benthamiana. In altered plants, a greater degree of tolerance was discovered (Shukla et al., 2018). Similarly, SpCas9 and sgRNA targeting the rep and coat proteins in a tomato plant and N. benthamiana were used to induce viral resistance against tomato yellow leaf curl virus (TYLCV) (Pramanik et al., 2021). Additional research has demonstrated improvements in resistance to wheat dwarf virus (WDV) and banana streak virus (BSV) via the use of CRISPR/SpCas9 to target conserved genomic regions (Ji et al., 2019; Wang et al., 2022).

Therefore, CRISPR allows direct interference with viral genomes and represents an effective approach to control plant viral diseases.

5.2 Insect resistance mechanisms

Insect pests, like other biotic stressors, have raised significant concerns regarding yield losses, jeopardizing agricultural output. Farmers have, however, embraced chemical pesticides for insect pest management, the extensive use of which can be detrimental to humanity and the environment. The use of biotechnology is crucial for controlling insect pests to protect crops and increase crop yields. Genome-editing technology makes use of the internal mechanisms of cells. Biotechnology has implications for controlling insect pests because it can change the way a gene functions. Genome editing is the process of changing the DNA sequence of a target genome by adding new bases or eliminating or swapping out existing bases (Komal et al., 2023). The CRISPR/Cas9-based two-component genome editing system offers a versatile platform for genome editing, enabling advancements in crop resistance against insects and pathogens. Strategies include modifying effector–target interactions, silencing host susceptibility genes, developing synthetic immune receptors for broad-spectrum resistance, and uncoupling antagonistic hormone actions. Additionally, insect genome modification can facilitate gene drive strategies or overcome insecticide resistance (Bisht et al., 2019).

Plants can be engineered via CRISPR/Cas systems to either generate or inhibit specific enzymes that repel insect pests or attract particular insect predators that prey on the bug species that infest the plant (Moon et al., 2022). Insects select host plants for egg laying on the basis of the availability of food for their offspring, guided by plant volatile blends that act as cues. Owing to their keen olfactory systems, suitable plants can be detected via the sensing of volatile secondary chemicals. Research indicates that modifying these volatile mixtures through genome editing can render plants resistant to insects and even lethal to them (Beale et al., 2006). The development of insect resistance in plant species through the editing of R and S genes is an increasingly reliable approach. Genetic engineering has shown success in creating insect pest resistance in plants by inactivating S genes. For example, deleting the tryptamine 5-hydroxylase encoding the CYP71A1 gene with CRISPR–Cas led to the conversion of tryptamine to serotonin in plants, thereby inhibiting hopper growth. Similarly, rice was modified via CRISPR-Cas9 technology to achieve resistance against the striped stem borer and the brown plant hopper (Lu et al., 2018). Interestingly, studies have shown that alterations in plant coloration can influence insect host selection. For example, gene editing of the anthocyanin pathway in tobacco results in red foliage, which disrupts host recognition by pests such as Helicoverpa armigera and Spodoptera litura, thereby conferring insect tolerance (Moon et al., 2022).

Owing to the effective genome editing of the well-known model organism Drosophila melanogaster, the CRISPR/Cas technique has attracted much interest in the entomology community. Since then, CRISPR/Cas has been successfully used on a variety of insects, such as Bombyx mori, Anopheles gambiae, and Plutella xylostella (Xu et al., 2025). Genome editing in insects can be effectively utilized through a two-step technique that involves modifying target insects and subsequently releasing them into the natural environment (Tyagi et al., 2020). To escape the controversial Bt technology, efforts are being made to engineer receptors so that resistance management can be efficacious. Evidence of effective genome editing in Helicoverpa armigera is provided by the knockdown of cadherin receptors that are genetically associated with Cry1Ac toxin tolerance (Wang et al., 2016). The development of insect resistance is significantly influenced by CYP genes, which are essential components of metabolic detoxifying enzymes in insects. CYP6G1 and CYP6G2 are important candidate genes in D. melanogaster that are involved in metabolism and resistance to insecticides. Imidacloprid resistance is conferred via high expression of the CYP6G1 and CYP6G2 genes, which are knocked out via CRISPR/Cas9 (Denecke et al., 2017). In addition to D. melanogaster, drug resistance in other agricultural pests, such as H. armigera, Spodoptera exigua, and Plutella xylostella, has also been studied via CRISPR/Cas technology. By using CRISPR/Cas9 technology to knock out resistance-related genes, including cadherin, P450, and GST genes, in various pests, researchers have been able to elucidate the functions of these genes in pest resistance (Xu et al., 2025). However, CRISPR technology also offers a wide range of potential applications in the management of public health pests. Reducing the ability of vectors to carry diseases and sterilizing insect populations are the two main methods suggested to stop the spread of viruses carried by mosquitoes. CRISPR/Cas9 research has revealed that membrane proteins and their mutations are important contributors to resistance to insecticides and may be targets for the development of novel mosquito-borne disease control strategies (Shaw and Catteruccia, 2019). CRISPR/Cas9 technology has the potential to create new pesticides in addition to reversing resistance. By altering genes linked to drug metabolism, drug targets, or drug transport in insects, scientists can create effective, low-toxicity chemical or biological insecticides that are suitable for particular insect species (Gouda et al., 2024).

6 Challenges and limitations

6.1 Technical challenges

While CRISPR/Cas9 and relevant genome‐editing platforms have the potential to transform crop improvement and biofortification, several technical challenges (Figure 2) need to be overcome before their routine application in agricultural practice. First, off‐target mutagenesis is still a serious issue, which is more common in plants (≥50%) than in animals and humans (Angon et al., 2023). High‐fidelity Cas9 variants such as eSpCas9, SpCas9-HF1 and FrCas9 and engineered base editors substantially decrease off‐target cleavage; however, even low‐frequency off‐targets can generate detrimental phenotypes or disrupt agronomic traits, requiring exhaustive genome‐wide specificity assays and long backcrossing schemes to remove spurious edits (Hajiahmadi et al., 2019; Chen et al., 2024).

Moreover, not only off-target mutations but also on-target edits can sometimes result in unanticipated phenotypic consequences. Various target genes exhibit pleiotropic effects with positive and negative influences on crop production at the same time because their expression is individually spatiotemporally controllable by a combination of cis-regulatory elements (CREs) and trans-acting factors. For example, a gene whose mutation increases grain number but simultaneously decreases 1000-grain weight does not contribute greatly to an increase in crop yield (Cui et al., 2023). Another major challenge is PAM dependency. PAM sequences enhance specificity while restricting tractable sites. PAM-free systems enable a wider editing range but leave room for greater off-target effects (Zhu et al., 2020).

The efficiency of the delivery of editing reagents into a wider variety of crop species, particularly those for which transformation remains a recalcitrant impediment, still curtails their application (Chen et al., 2024). Methods such as traditional Agrobacterium‐mediated transformation and biolistics may have low editing efficiency, involve tissue culture steps that induce somaclonal variation, and depend on the genotype. New delivery strategies based on nanoparticles and DNA‐free ribonucleoproteins, which are predicted to circumvent these limitations, necessitate large scale, reproducibility, and low cytotoxicity (Wei et al., 2020; Chen et al., 2024).

The design and efficiency of multiplexed editing of polygenic and homeologous loci in complicated genomes, such as those of hexaploid wheat, constitute another significant technical challenge (Li et al., 2021). Packing multiple guide RNAs into a single vector may lead to competition between guide RNAs, preferential editing of some targets over others, and unpredictable epistatic interactions or mutations at the target sites (Sánchez-León et al., 2024). To enable balanced editing in each allele without off‐target activation of paralogous genes, more precise computational tools for guiding selection, more repeat‐able expression cassettes, and robust control of the activity of the Cas nuclease are needed.

Detecting off-target and unintended on-target effects is itself harder in polyploid crops than in diploids. In hexaploid wheat or octoploid strawberry, homeologous copies of a target gene across sub-genomes are often 95–99% identical, so standard whole-genome resequencing and alignment pipelines struggle to distinguish a true off-target edit at a homeolog from a genuine on-target edit — without careful sub-genome-resolved variant calling, off-target rates in polyploids can be systematically underestimated (Sánchez-León et al., 2024; Li et al., 2021). Editing efficiency is also strongly genotype-dependent: the same construct and guide RNA can produce high editing rates in a transformation-amenable genotype (e.g., japonica rice, Kitaake) and near-zero rates in an elite or recalcitrant genotype, because transformation efficiency, tissue-culture regenerability, and chromatin accessibility at the target locus all vary by background (Chen et al., 2024). This means that a validated edit in a model or reference genotype cannot be assumed to transfer efficiently into the elite germplasm actually used by breeders, adding a genotype-retargeting step to nearly every deployment pipeline.

CRISPR-based plant gene editing faces another major technological impediment linked to the extremely low efficiency of homology-directed repair (HDR), which is required for precise modification of a DNA sequence (Molla et al., 2022). Since HDR events are very rare in plants, the double-strand breaks caused by the CRISPR machinery are typically mended through the alternative nonhomologous end joining (NHEJ) pathway. Although NHEJ is a highly error-prone repair mechanism and often results in random insertions or deletions at the target site, a low frequency of HDR leads to challenges associated with insufficient accuracy in making changes (Molla et al., 2022).

Compared with coding-sequence editing, precise regulatory sequence engineering, such as tuning promoter strength and changing UTRs to control gene dosage, remains in its infancy. While recent prime editing and transcriptional modulation platforms can exploit subtle cis‐regulatory changes, further progress has been hampered by poor in‐planta efficiency and low predictability of effects on transcript abundance and downstream metabolic fluxes (Gan and Ling, 2022).

In addition to these technical challenges, issues such as random insertion sites of the targeted DNA, limited targetable protein sites, bystander editing, and ethical, biosafety, and regulatory questions impose additional hurdles (Angon et al., 2023). Overcoming these technical hurdles must be achieved if CRISPR‐mediated crop improvement is to transition from proof‐of‐concept studies to dependable and fieldable strategies that sustainably increase yield, resilience and nutritional value.

6.2 Regulatory and commercialization challenges

A major practical barrier to deploying CRISPR-edited crops is jurisdictional rather than technical: regulatory treatment varies sharply across countries, and that variation reflects two competing philosophies. Product-based frameworks, exemplified by the USDA’s 2018 determination, regulate the trait itself and exempt edits that introduce no foreign DNA and could plausibly arise through conventional breeding; under this approach, many CRISPR-edited crops are not classified as GMOs and do not undergo federal biosafety review (Waltz, 2018; Bhowmik et al., 2021). Process-based frameworks, by contrast, regulate the method used to create the trait regardless of the final product’s composition. The European Union is the clearest example: following the Court of Justice ruling in Confédération Paysanne (C-528/16), genome-edited organisms were brought under Directive 2001/18/EC and subjected to the same risk-assessment pathway as transgenic crops (Purnhagen and Wesseler, 2021; Siebert et al., 2021). That ruling appears to have had a chilling effect on investment, with Bayer and BASF publicly shifting gene-editing activity away from the EU and smaller breeding companies following suit by the end of 2018 (Bhowmik et al., 2021). Table 6 summarizes where major agricultural economies currently fall on the product-based/process-based spectrum.

Table 6. Regulatory treatment of CRISPR-edited crops by jurisdiction.

The regulatory divide also matters for food-security applications: 13 WTO members have issued a joint statement supporting streamlined regulation of gene-edited agricultural products, an early step toward international harmonization, but no binding global standard yet exists (Kumar et al., 2022). Because gene-edited crops have not shown health or environmental harms distinct from conventionally bred crops over more than two decades of GM crop use (Das et al., 2023), several scholars argue that regulation should track the risk profile of the resulting trait or product rather than the editing technology used to generate it, a product-based logic that would align oversight more closely with actual risk than the current process-based EU model (Hartung and Schiemann, 2014; Podevin et al., 2012).

6.3 Socioeconomic considerations

CRISPR technology holds immense potential for agriculture, but it also raises difficult ethical and regulatory challenges. The ability to edit genomes in crops such as rice and wheat precisely and rapidly to improve yields or nutritional content has sparked debate over the moral acceptability of altering plant genomes. These concerns are especially strong in regions such as Europe, where public attitudes toward genetic modification remain cautious. Ethical discussions focus on issues such as unintentional consequences, the perception of creating “unnatural” organisms, and potential long-term effects on biodiversity and ecosystems (Marone et al., 2023). These uncertainties demonstrate the importance of healthy ethical frameworks and internationally harmonized regulations that balance innovation with responsibility. At times, questions of access and equity complicate the picture. The global patent landscape, dominated by the United States and European unions, has created barriers for smaller institutions and developing countries; as a result, CRISPR-edited tomatoes enriched with GABA, where restrictive patents could limit access in less affluent regions (Akhtar et al., 2023). The concentration of CRISPR technologies within a handful of corporations risks deepening inequalities in global agriculture, especially for staple crops such as maize and wheat, which are central to food security in the Global South (Molinari et al., 2024). Countries such as India and several African countries now face the challenge of ensuring that benefits from CRISPR-based innovations, whether drought-tolerant maize or disease-resistant cassava, are widely accessible to farmers beyond large agribusinesses (Munawar et al., 2024).

Governance questions become sharper as editing complexity increases. Multiplex editing, which stacks several simultaneous genomic changes to address polygenic traits, compounds the off-target and unintended-interaction concerns discussed in Section 6.1, yet most existing national frameworks (Table 6) were written with single-gene edits in mind and do not explicitly define how many stacked or simultaneous edits still qualify for exemption from GMO-equivalent review (Sampath et al., 2023). A more acute governance gap concerns gene drives — self-propagating genetic elements capable of spreading a trait through a wild or semi-domesticated population far faster than Mendelian inheritance would allow. While gene drives have been discussed mainly for insect vector control, their conceptual extension to agricultural pest management (e.g., suppressing insect pest populations that vector plant pathogens) raises distinct ecological and containment concerns that current crop-focused biosafety frameworks are not designed to evaluate, since a released drive is, by design, difficult to recall once it begins spreading through a population (Marone et al., 2023). No jurisdiction reviewed in Table 6 currently has a gene-drive-specific approval pathway for agricultural applications, leaving this as an open regulatory and ethical question rather than a resolved one.

The identification of consumer priorities for gene-edited foods is important; any negative attitudes can hinder acceptance and public health benefits. Gulyas et al. (2024) reported that consumers worldwide expressed a willingness to pay an average premium of 23.9% for genetically modified biofortified crops, particularly when positive information about their advantages was presented.

7 Future directions and emerging technologies

The combination of CRISPR and precision agriculture has led to a transformative step toward sustainable and efficient farming, emphasizing targeted crop modifications to improve yield, resistance to diseases, and tolerance to environmental stresses (Sampath et al., 2023; Schnurr, 2019). CRISPR can help create “smart crops” that respond to precision agriculture systems, delivering real-time information about their health and requirements (Rai, 2022).

To achieve the agronomic benefits of genome-edited crops, precision or smart farming methods, such as robotics, artificial intelligence, and IoT technologies, are necessary to increase sustainability and yield better yields (Sharma et al., 2023). IoT-based systems provide farmers with the ability to collect real-time data on crop health, soil conditions, and climate, as well as field-specific decisions on irrigation, fertilization, and pesticide use. By merging sensors, drones, and AI-driven data analysis, these networks collect information on soil moisture, acidity, and nutrients with aerial and environmental inputs, which helps to predict stress factors and optimize farm management (Sharma et al., 2023). Mobile applications are especially valuable in addressing knowledge gaps, particularly in areas with limited access to computers and other communication technologies (Ayim et al., 2022). As climate change is turning agriculture into new environments and genome-edited crops are being adapted to extreme conditions, robotics will play a key role in supporting the cultivation and management of these crops (Botta et al., 2022). The application of robotic systems with genome-edited crops can increase productivity, aligning agriculture with advances in plant science to meet the demands of an increasing population under climate change. Combining precision and smart farming with genome editing may help overcome yield gaps, improve crop quality, and lower environmental impacts with social, economic, and ecological benefits (Bradbury et al., 2025).

CRISPR-Cas9 is an effective tool that enables precise modifications of DNA sequences, transforming biological research. However, several challenges, such as selecting the best target sites, minimizing unintended off-target effects, and managing the extensive amount of genomic data, exist. Artificial intelligence (AI) can address these issues by analyzing massive datasets, recognizing complex patterns, and providing predictive models that can improve the accuracy and effectiveness of CRISPR-Cas9 applications (Saini et al., 2025; Goshisht, 2024). AI models are trained to use large datasets to predict off-target sites. By integrating these predictions, scientists can develop more precise CRISPR systems that reduce unintended genetic modifications (Zhang et al., 2023).

Considerable progress has been made by combining AI with CRISPR-Cas9, but several challenges, such as data quality, computational resources, and the interpretability of AI models, still exist. Moreover, ethical concerns related to both genetic editing and AI applications should be considered. Future research should address these obstacles, enhance AI methodologies, and widen the applications of CRISPR technology.

8 Conclusions

To ensure food security and agricultural sustainability in the context of severe weather, it is essential to develop crops that are climate resilient with high nutritional value. Breeding strategy advancements, ranging from conventional techniques to state-of-the-art gene editing technologies, offer encouraging answers to this problem. Researchers can greatly increase the resilience of crops to climate change by combining genetic variety with contemporary phenotyping and genotyping methods and concentrating on breeding for resistance to multiple stresses. Despite the uncertainties brought about by a changing climate, these initiatives will not only preserve crop yields and quality but also support the stability of global food systems by guaranteeing that agricultural production can satisfy the demands of an expanding population.

Considering the new development of CRISPR technology and the extensive duration required to create commercial crop varieties and navigate regular regulatory processes, it is imperative to reassess the regulatory timeframe. Furthermore, the existing legal framework in the EU classifies CRISPR crops as genetically modified organisms, notwithstanding the absence of transgenes and foreign DNA in the products (Zaidi et al., 2020). These laws and regulations increase the duration and expense of variety creation. Scientists and politicians must collaborate to formulate comprehensive strategies for the integration of CRISPR crops.

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Footnotes

Edited by: Guanglian Liao, Jiangxi Agricultural University, China

Reviewed by: Obaid Ur Rehman, Zhejiang University, China

J. Jorben, Banaras Hindu University, India