Genome Editing for Climate Change Adaptation in Agriculture: Innovations, Applications, and Regulatory Considerations

Koppolu Raja Rajesh Kumar^1*Prashant Kumar Singh²

• ¹Indira Gandhi National Tribal University, Amarkantak, India
• ²University of Lucknow, Lucknow, India

Human-induced climate change has unequivocally altered the global climate system, with surface temperatures rising by approximately 1.1°C above pre-industrial levels during 2011-2020, and warming occurring more rapidly over land than oceans. This rise is already manifesting in widespread changes to weather and climate extremes across all regions, including more frequent and intense heatwaves, droughts, heavy precipitation and flooding (IPCC 2023). Agriculture, in particular, is highly vulnerable to these changes, as climate-driven increases in drought and flooding threaten crop productivity, food security, and rural livelihoods. Moreover, the increasing frequency and intensity of climate extremes are expected to heighten the probability of concurrent yield losses across major food-producing regions (Bezner Kerr et al. 2022). While adaptation strategies such as water management, agroforestry, and the development of improved cultivars are being implemented, the scale and urgency of the climate challenge necessitate innovative solutions that can deliver resilient and sustainable agricultural systems. The integration of CRISPR/Cas9 genome editing into crop improvement programs represents one of the most significant advances in agricultural biotechnology, offering unprecedented precision to accelerate the breeding of climate-resilient varieties.Recent advances in genome editing technologies, together with the integration of genomics, phenomics, and artificial intelligence (AI) / machine learning (ML), offer significant opportunities for agricultural improvement. The four research articles published under the research topic highlight essential aspects of this transformative technology, from technical optimization to regulatory frameworks.A fundamental requirement for successful genome editing is the design of highly specific guide RNAs (gRNAs), which direct the Cas9 nuclease to the intended genomic target. gRNA design is particularly challenging in wheat due to its complex allohexaploid genome, large genome size (~17 Gb), and a high proportion of repetitive sequences. These factors, along with the prevalence of multi-gene families, complicate target recognition and elevate the risk of offtarget activity. Effective editing thus depends not only on selecting the correct gene target but also on optimizing gRNA design and addressing post-design considerations such as gRNA stability, binding efficiency, and functional performance. Addressing these challenges, the methods article by Singh et al. (2025) presents a consolidated and detailed workflow for efficient gene selection and gRNA design in wheat, using the TaARE1 gene as an example. The authors systematically evaluate structural, physical, compositional, and free energy parameters through advanced bioinformatic tools to identify gRNAs with high on-target activity, and minimal off-target effects. Wheat, being a staple food crop for a significant portion of the global population, can benefit from this comprehensive toolkit, which provides practical guidance for navigating the complexities of genome editing and developing improved varieties that are adaptable to climate change.Following the selection of the target gene and the design of recombinant vectors expressing gRNA and Cas9 or other RNA-guided endonucleases, a crucial subsequent step is the efficient delivery and transformation into plant cells using techniques such as Agrobacterium tumefaciens-mediated transformation or biolistic bombardment. However, this step represents a significant bottleneck in plant genome editing, as many crops require specialized transformation and regeneration protocols based on tissue culture. These processes are not only time-consuming and labor-intensive but also species-dependent. In contrast, in planta transformation methods have emerged as promising alternatives that bypass many of these challenges by targeting meristematic tissues, floral structures, or embryos directly, thereby reducing or eliminating the need for tissue culture steps. Additionally, success of novel approaches like de novo meristem induction, spray-on genome editing using carbon dotrecombinant plasmid complexes, and regenerative activity-dependent in-planta injection delivery (RAPID)-in some crop species further expand the possibilities for efficient gene editing in essential crops. In their review, Sebiani-Calvo et al. further emphasize its role in fruit, vegetable, and tuber crops, with significant potential for improving agriculture in Peru. In their review, Mestanza et al. (2025) highlight the advances in CRISPR/Cas9 genome editing and its wide-ranging applications across diverse crop types in Peru, with a particular focus on transgene-free approaches. They discuss how CRISPR technologies, in addition to cereal crops, have been successfully applied to improve fruit crops by enhancing traits such as disease resistance and shelf life; vegetable crops by optimizing stress tolerance and nutrient content; and tuber crops-especially potatoes-by addressing climate-related challenges such as heat stress, drought, and pest infestations. These innovations are particularly relevant to Peru's diverse agroecosystems, where regions like the Andean face chronic drought affecting staple crops such as potato, maize, quinoa, and beans. The authors also emphasize biofortification as a promising strategy to combat chronic malnutrition, which remains a pressing issue in vulnerable rural populations. Central to these efforts is the adoption of transgene-free genome editing strategies, such as the direct delivery of ribonucleoprotein (RNP) complexes, and incorporation of tRNA-like sequence (TLS) motifs into the single guide RNA (sgRNA) of the CRISPR/Cas system which enable precise genetic modifications without introducing foreign DNA into the plant genome. These approaches are especially significant in Peru, where regulatory frameworks are cautious regarding genetically modified organisms (GMOs), and a national moratorium imposes strict biosafety provisions. By leveraging transgene-free techniques, researchers can navigate these regulatory barriers, facilitating the development of crop varieties that exhibit improved resilience to biotic and abiotic stresses, enhanced nutritional profiles, and reduced reliance on agrochemicals like pesticides. Mestanza et al. advocate for a collaborative approach, emphasizing that cooperation among scientists, legislators, and farmers is essential to creating a robust regulatory framework that encourages technological innovation while safeguarding environmental sustainability and public health. Such a framework would enable the responsible adoption of genome editing technologies, contributing to food security and sustainable agriculture across Peru's challenging and varied agricultural landscapes. Notably, some countries now exempt SDN-1 or SDN-2 edits from GMO oversight, accelerating their adoption. India has recently joined countries such as the United States, Japan, Canada, China, and the Philippines in approving genome-edited crops, with its first such rice varieties now approved.The programmable RNA-guided endonuclease toolkit is rapidly expanding, enabling significant breakthroughs in genome editing for scientific research and biotechnological innovation. For example, a small, programmable RNA-guided gene-editing system called TIGR-Tas (Tandem Interspaced Guide RNA-Targeting Systems) was recently reported to overcome key limitations of CRISPR (Faure et al., 2025). Unlike CRISPR, which requires PAM sequences to target genes, TIGR-Tas is PAM-independent, potentially broadening the targetable genome. Its compact size and dual-guide mechanism, which interacts with both DNA strands, may improve precision and reduce off-target effects compared to single-guide RNA systems. These innovations illustrate how continuous technological advancement is expanding the precision, scope, and accessibility of genome editing. While such tools offer potential solutions to food security and sustainability challenges, concerns persist regarding intellectual property monopolies and equitable access for smallholder farmers. Furthermore, given the rapid pace of technological innovation, rigorous evaluation of biosafety and ecological impacts is critical to ensure that genome-editing technologies are deployed safely and sustainably (Kumar, 2025).