Genome editing in Agriculture: CRISPR/Cas9’s promise in creating resilient and high-yielding crops

Vinod Kumar¹ , Virendra Bahadur² , Satish K. Sharma³ , Pradip Kumar Saini⁴ , Amol M Tripathi⁵

¹IARI- National Institute for Plant Biotechnology, New Delhi, India.

²Department of Genetics and Plant Breeding, Ganpat Sahaai PG College, Uttar Pradesh-India.

³Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Jammu, Jammu and Kashmir 180009, India.

⁴Acharya Narendra Deva University of Agriculture and Technology, Kumarganj, Ayodhya (Uttar Pradesh) India.

⁵Nehru gram Bharati Institute (NGBU) Prayagraj, Uttar Pradesh, India.

Corresponding Author Email: sharmavinod612@gmail.com

DOI : https://doi.org/10.51470/ABP.2023.02.03.17

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Introduction

In the face of a growing global population and the unpredictable impacts of climate change on agricultural productivity, there is an increasing need to develop crops that are resilient to environmental stressors and capable of yielding higher harvests. This challenge has led to the emergence of genome editing technologies as promising tools to revolutionize agriculture. Among these technologies, the CRISPR/Cas9 system has garnered significant attention due to its precision, efficiency, and versatility in making targeted modifications to plant genomes [1]. The CRISPR/Cas9 system, inspired by the bacterial immune system, consists of two main components: the single-guide RNA (sgRNA) that guides the Cas9 enzyme to a specific genomic target, and the Cas9 nuclease that induces double-strand breaks at the target site. This breakage prompts the cellular DNA repair machinery to either introduce errors, leading to gene disruptions or incorporate desired changes through homology-directed repair. This mechanism provides researchers with a precise and customizable means to alter specific genes, enabling the development of crops with enhanced traits [2]. The applications of CRISPR/Cas9 in agriculture are broad and impactful. Beyond conventional breeding methods that are often time-consuming and labor-intensive, CRISPR/Cas9 allows for the direct manipulation of target genes, enabling the development of crops with improved traits such as disease resistance, drought tolerance, and nutrient utilization efficiency. Moreover, the ability to silence or modify genes responsible for undesirable characteristics offers a way to eliminate allergens or anti-nutritional compounds from crops, thus enhancing food safety and quality [3]. As researchers continue to harness the power of CRISPR/Cas9, the potential to create crops that are both resilient and high-yielding becomes increasingly feasible. By introducing genetic modifications that bolster plants’ ability to withstand biotic stresses caused by pests and diseases, as well as abiotic stresses like extreme temperatures and limited water availability, CRISPR-edited crops could contribute to greater agricultural sustainability and global food security [4-5].

In the subsequent sections of this review, we will delve deeper into the mechanisms and applications of CRISPR/Cas9 technology, focusing on how it can enhance crop resilience and optimize yields. We will also discuss the ethical and regulatory considerations surrounding the use of CRISPR-edited crops in agricultural systems, shedding light on the broader implications of this revolutionary technology [6].

CRISPR/Cas9 Technology: Mechanisms and Applications

The CRISPR/Cas9 system, a revolutionary genome editing tool, has found extensive application in agriculture due to its precise and efficient mechanisms. This section delves into the underlying mechanisms of the CRISPR/Cas9 technology and explores its diverse applications in the realm of agriculture.The CRISPR/Cas9 system is based on the bacterial adaptive immune response, where Cas9, an endonuclease enzyme, is guided to specific DNA sequences by a single-guide RNA (sgRNA) molecule. The sgRNA comprises a customizable sequence that is complementary to the target DNA site, directing Cas9 to introduce a double-strand break at that location. Subsequently, cellular repair mechanisms, such as non-homologous end joining (NHEJ) or homology-directed repair (HDR), are engaged [7]. NHEJ often results in insertions or deletions (indels) at the break site, leading to gene disruption. On the other hand, HDR can be exploited to incorporate specific genetic modifications at the target site, allowing for precise gene editing.

Applications in Agriculture: CRISPR/Cas9’s versatility has enabled a multitude of applications in agriculture, revolutionizing crop improvement strategies. One prominent application is the development of crops with enhanced disease resistance. By targeting susceptibility genes or introducing beneficial mutations, researchers have successfully generated plants with improved immunity against various pathogens. For example, in rice, the disruption of the susceptibility gene OsSWEET14 using CRISPR/Cas9 resulted in enhanced resistance against bacterial blight [8]. CRISPR/Cas9 technology has also proven effective in developing crops resilient to abiotic stresses. By modifying genes involved in stress response pathways, such as those regulating drought tolerance or salt resistance, researchers have created plants better equipped to withstand harsh environmental conditions. These genetically modified crops hold the potential to ensure stable yields even in challenging climates, contributing to global food security [9]. Furthermore, CRISPR/Cas9-mediated genome editing enables the optimization of crop traits related to yield and nutritional content. Through the targeted enhancement of genes associated with traits like yield-related hormones or nutrient uptake efficiency, researchers have achieved improved crop productivity. This technology has been used to create crops with higher yields, larger fruits, and enhanced nutritional profiles, addressing both quantity and quality aspects of agricultural production [10]. The CRISPR/Cas9 technology’s mechanisms of precise gene editing have unlocked a realm of possibilities for agriculture. Its applications span from disease resistance to stress tolerance and yield optimization, offering solutions to the challenges posed by evolving agricultural demands. The following sections of this review will further explore the utilization of CRISPR/Cas9 in enhancing crop resilience and maximizing yields.

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Enhancing Crop Resilience with CRISPR/Cas9

Climate change, coupled with escalating pest and disease pressures, poses formidable challenges to global agricultural productivity. In this context, the CRISPR/Cas9 system has emerged as a beacon of hope, offering the potential to bolster crop resilience through targeted genetic modifications [11]. This section delves into how CRISPR/Cas9 technology is being harnessed to enhance crop resilience against biotic and abiotic stresses.Pests and pathogens threaten crop yields worldwide, often requiring the use of chemical pesticides that are detrimental to both the environment and human health. CRISPR/Cas9 provides an innovative approach to develop crops resistant to biotic stresses. By targeting genes involved in plant-pathogen interactions, researchers have succeeded in generating plants with heightened resistance. For instance, in tomatoes, the disruption of the gene SlERF4 using CRISPR/Cas9 resulted in increased resistance against Botrytis cinerea, a common fungal pathogen [12]. Furthermore, the technology allows for the modification of susceptibility genes exploited by pests for infestation. By altering these genes, researchers can create crops less favorable to pests, reducing the need for chemical interventions. This approach has been demonstrated in maize, where CRISPR/Cas9-mediated mutation of a gene involved in insect attraction led to reduced damage caused by the European corn borer [13]. Abiotic stresses, such as drought, salinity, and extreme temperatures, severely constrain agricultural productivity. CRISPR/Cas9 provides a means to develop crops capable of thriving in adverse environmental conditions. By targeting genes involved in stress response pathways, researchers can enhance plants’ ability to tolerate or recover from abiotic stress. For instance, in rice, the modification of the OsMYB2 gene using CRISPR/Cas9 led to improved drought tolerance and enhanced yield under water-limited conditions [14].

Moreover, CRISPR/Cas9 technology enables the optimization of plant architecture for improved abiotic stress resilience. By modifying genes regulating root development, water uptake efficiency, and stomatal regulation, researchers have created crops better equipped to endure water scarcity and other stressors. These modified crops hold promise for sustained agricultural productivity in regions susceptible to climatic variations [15]. CRISPR/Cas9 technology offers a transformative approach to enhancing crop resilience against both biotic and abiotic stresses. By precisely targeting specific genes involved in stress responses, researchers are paving the way for the development of crops capable of thriving in challenging environments. As we proceed to the subsequent section, we will explore how CRISPR/Cas9 is utilized to optimize crop yields, contributing further to the advancement of agriculture.

Optimizing Crop Yields Using CRISPR/Cas9

In the pursuit of global food security, enhancing crop yields is paramount. The advent of the CRISPR/Cas9 technology has provided a powerful toolkit for precise genome editing, offering new avenues to optimize crop productivity. This section explores how CRISPR/Cas9 is being harnessed to maximize crop yields by targeting key genes and traits associated with enhanced agricultural output.

Yield-Related Hormones and Pathways: CRISPR/Cas9 technology has enabled researchers to modify genes involved in various plant growth and development pathways, thereby influencing yield-related traits. One prominent example is the manipulation of gibberellin biosynthesis genes to regulate plant height and grain size. In rice, mutations in the gene SD1, which encodes a gibberellin biosynthesis enzyme, have led to reduced plant height and improved lodging resistance, ultimately resulting in increased grain yield [16].

Furthermore, CRISPR/Cas9-mediated alterations in hormone signaling pathways can impact flowering time, fruit development, and seed production. By targeting genes controlling these processes, researchers can fine-tune crop growth cycles and synchronize them with optimal environmental conditions, ultimately boosting yields. The precision offered by CRISPR/Cas9 ensures that these modifications are specific and tailored to each crop’s requirements.

Nutrient Utilization Efficiency: Efficient nutrient utilization is vital for achieving high crop yields. CRISPR/Cas9 technology allows researchers to enhance the nutrient uptake and utilization efficiency of plants by targeting genes involved in nutrient transport, assimilation, and storage. For instance, in wheat, CRISPR/Cas9-mediated mutation of the TaGAMYB gene led to increased grain size and higher grain Zn and Fe concentrations, addressing both yield and nutritional quality simultaneously [17]. By optimizing nutrient utilization pathways, CRISPR-edited crops can thrive in nutrient-deficient soils, reducing the reliance on external fertilizers and minimizing the environmental impact associated with excessive fertilizer application.

Photosynthesis Enhancement: Photosynthesis, the fundamental process by which plants convert sunlight into energy, is a key determinant of crop yields. CRISPR/Cas9 technology offers the potential to improve photosynthetic efficiency by targeting genes related to photosynthesis pathways. Researchers have successfully enhanced crop yields by modifying genes involved in carbon fixation, electron transport, and Rubisco activity, leading to increased biomass production [18]. CRISPR/Cas9 technology holds immense promise for optimizing crop yields by targeting genes and pathways that influence growth, development, nutrient utilization, and photosynthesis. This precision editing approach provides a means to fine-tune crops for maximal productivity while minimizing the ecological footprint of agriculture. In the subsequent section, we will delve into the ethical and regulatory considerations surrounding the use of CRISPR-edited crops in agriculture.

Ethical and Regulatory Considerations for CRISPR-Edited Crops

The rapid advancement of CRISPR/Cas9 technology in agriculture has ushered in a new era of crop improvement, but it also raises important ethical and regulatory questions. As society embraces the potential of CRISPR-edited crops to address pressing challenges, such as food security and sustainability, it is crucial to navigate these considerations to ensure responsible and equitable deployment.

Environmental Impact: CRISPR-edited crops could have unintended ecological consequences, such as unintended gene flow to wild relatives or disruption of local ecosystems. Ethical evaluations must address potential impacts on biodiversity and ecosystem stability [19]

Unintended Effects: While CRISPR is highly precise, off-target effects can occur. Ethical concerns arise regarding the potential introduction of unintended genetic changes that may have unforeseen health or environmental implications [20].

Equity and Access: The equitable distribution of benefits from CRISPR-edited crops is a central ethical concern. Ensuring that developed crops benefit smallholder farmers and disadvantaged regions is crucial to avoiding exacerbation of existing social inequalities [21].

Transparency and Public Engagement: Ethical considerations emphasize the importance of transparent communication with the public. Engaging communities, consumers, and stakeholders in discussions about the potential risks and benefits of CRISPR-edited crops is essential for informed decision-making [22].

Fig 1: CRISPR/Cas9 technology enables precise genetic modifications to bolster plant productivity amidst challenging environmental conditions. Using a single guide RNA (sgRNA), the Cas9 protein is directed to specific genomic regions of interest. Within the CRISPR/Cas9 system, identification of a G-rich protospacer adjacent motif (PAM) region adjacent to the target DNA facilitates cleavage, resulting in a blunt-ended double-stranded break (DSB). These breaks prompt the plant’s inherent repair mechanisms, which can engage non-homologous end joining (NHEJ) or homology-directed repair to mend the DNA. CRISPR/Cas9 induces mutations such as insertions or deletions (INDELs), gene deletions, and multiplex gene knockouts, thereby offering a potent approach for precise genetic manipulation in plants. Adopted by [28] Copyright permission from MDPI.

Regulatory Considerations:

GMO Regulations: The regulatory status of CRISPR-edited crops varies globally. Many countries treat them similarly to genetically modified organisms (GMOs), necessitating rigorous safety assessments and labeling. Regulatory frameworks must keep pace with technological advancements to ensure accurate categorization [23].

Traceability and Labeling: Clear labeling of CRISPR-edited products enables consumer choice and informed decision-making. Developing consistent labeling standards and mechanisms is essential to maintain transparency and build trust [24].

Risk Assessment: Robust risk assessment procedures are required to evaluate the potential unintended effects of CRISPR-edited crops. Balancing scientific innovation with the need for comprehensive safety evaluations is critical [25].

Intellectual Property: The intellectual property landscape surrounding CRISPR-edited crops raises concerns about accessibility, particularly for small-scale farmers in developing countries. Balancing intellectual property rights with the public good is a regulatory challenge [26].

International Harmonization: The global nature of agricultural trade necessitates international cooperation in regulatory frameworks. Harmonizing regulations ensures that CRISPR-edited crops can be traded and accepted across borders [27]. The adoption of CRISPR-edited crops in agriculture brings forth both exciting possibilities and complex ethical and regulatory challenges. Responsible innovation requires an ongoing dialogue between scientists, policymakers, ethicists, and the public to ensure that CRISPR technology is harnessed for the greater good, while addressing concerns about safety, equity, transparency, and sustainability.

Conclusion

CRISPR/Cas9 technology, revolutionizing agriculture, offers a promising solution for developing resilient and high-yielding crops. This gene-editing tool enables precise genetic modifications, enhancing crop resilience to environmental stresses and diseases, and improving yields. CRISPR/Cas9 accelerates breeding processes, contributing to sustainable agricultural practices. However, its application is not without challenges, including ethical, regulatory, and public acceptance issues. The technology’s success in agriculture depends not only on its scientific capabilities but also on addressing these broader concerns effectively.

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