The use of CRISPR technology in food production

Introduction

When Ama’s maize fields turned to dust, she thought the land had given up on her. Then Dr Mensah arrived not with fertilizer or promises, but with an idea. He spoke of CRISPR, a gene-editing tool that could help crops survive drought and disease by rewriting nature’s own code. For the first time, science offered Ama something stronger than hope, a chance to fight back. Their meeting revealed a new truth about farming: the future of food may not lie solely in the soil, but in the power of innovation.

CRISPR Technology

CRISPR stands for “clustered interspaced short palindromic repeats.” Biologists use the term to describe the “genetic appearance” of a system, which was first discovered in microbes, including bacteria and archaea, as early as 1987. For a long time, no one really understood what it did, but around 2005, researchers discovered that CRISPR is an immune system. It’s used by microbes to help protect themselves from invading viruses. To stop the invaders, the microbes use CRISPR to recognize and eliminate specific trespassers.

It is believed that CRISPR  can have a positive impact on food production, quality, and environmental sustainability. This will be even more important as the world's population continues to grow, and less arable land and fewer water resources become available for crop production, in part due to climate change.

In addition to the aforementioned opportunities, genetic planning also has the potential to reduce the inputs needed to produce food, enhance our green energy production (especially from biodiesel), and provide a means to combat climate change through improved carbon sequestration. While CRISPR has the potential to cure some diseases, studies have shown that it can lead to genetic mutations that result in downsizing. If genetic engineering is performed in embryos, eggs, or sperm cells, these changes will benefit all future generations.

CRISPR-Cas9 technology is an effective genome editing tool that has been utilized to enhance the characteristics of key agricultural plants, including quality, disease resistance, and herbicide tolerance.

How CRISPR-Cas9 Operates

Scientists have realized they can harness this natural defense system to edit genes in plants, animals, and even humans. Here’s how it works:

1.      Guide RNA (gRNA): Researchers design a small piece of RNA that matches the specific DNA sequence they want to change. This acts like a GPS, guiding the Cas9 protein to the exact location in the genome.

2.      Cas9 Enzyme: Cas9 is a special protein that acts like molecular scissors. Once guided to the target site, it cuts the DNA at that precise spot.

3.      DNA Repair: After the DNA is cut, the cell’s natural repair process begins. Scientists can use this moment to add, remove, or replace specific genetic material — effectively rewriting the genetic code.

CRISPR-Cas9 stands out for its precision, cost-effectiveness, and speed. It can target and edit specific genes accurately, minimizing unwanted changes. The method is cheaper and simpler than older genetic engineering techniques, making advanced research more accessible. Most importantly, CRISPR enables rapid genetic improvements, allowing scientists to develop resilient crops and livestock in a fraction of the time required by traditional breeding methods.

 Applications of CRISPR in Crop Production

CRISPR/Cas9 system for breeding resistance and improving quality in tomato.

Specifically, in tomato (Solanum lycopersicum), CRISPR-Cas9 was used to modify SlJAZ2, producing a variant that prevents stomatal reopening and confers resistance to bacterial speck disease caused by Pseudomonas syringae pv. tomato DC3000. Editing of SlDmr6-1, the tomato equivalent of the Arabidopsis DMR6 gene, provided broad-spectrum resistance against multiple pathogens, including P. syringae, Phytophthora capsici, and Xanthomonas species.

For biotic stress resistance, genes like PMR4 and JAZ2 were edited to produce tomatoes resistant to powdery mildew and banana streak virus, while MAPK3 and DCL2b influenced susceptibility to fungal and viral pathogens. Additionally, edits to DELLA, BOP, TFAM, and SHR enhanced plant growth habits, root development, and tolerance to abiotic stresses, including drought and poor soil conditions. CRISPR/Cas9 system for breeding resistance and improving quality in citrus.

CRISPR has also demonstrated major success in citrus breeding. Editing the CsLOB1 gene disrupted activation by the bacterial effector PthA4 from Xanthomonas citri subsp. Citri, the pathogen responsible for citrus canker. This modification significantly reduced disease symptoms in grapefruit (Citrus × paradisi) and Wanjincheng orange (Citrus sinensis), representing a major breakthrough in developing disease-resistant citrus varieties.

Applications of CRISPR in Livestock Production

The creation and propagation of genome-edited animals using CRISPR technology rely heavily on advanced reproductive technologies. Among these, in vitro embryo production (IVEP) is the preferred method because it provides a sufficient number of high-quality zygotes suitable for microinjection with CRISPR components. Oocytes are collected either from live animals through follicular aspiration or from ovaries obtained at slaughterhouses. IVEP offers significant advantages over in vivo zygote collection, achieving fertilization and cleavage rates of around 80–90% and blastocyst development rates of about 30–40% under optimal laboratory conditions.

The CRISPR-Cas9 system has made genetic modification easier in livestock because it allows cytoplasmic microinjection instead of pronuclear injection, eliminating the need for centrifugation and visualization of pronuclei. This results in a simpler, faster, and less invasive process that improves embryo survival and editing efficiency.

Alternatively, somatic cell nuclear transfer (SCNT) combined with CRISPR-transfected donor cells can also be used to generate edited animals. However, SCNT is technically complex and has low efficiency, with high risks of developmental abnormalities, pregnancy failure, and low offspring survival. Despite this, when successfully performed, most resulting animals carry the desired genetic modifications.

Overall, direct microinjection of CRISPR components into zygotes is the most effective and widely used method across various species, including sheep, goats, and pigs, offering high editing rates, minimal developmental impact, strong pregnancy outcomes, and good newborn survival.

The CRISPR pipeline for transforming livestock involves using a single guide RNA (sgRNA) to direct the Cas9 enzyme to a specific DNA site, where it creates double-strand breaks. These breaks are repaired through either non-homologous end joining (NHEJ) or homology-directed repair (HDR) if a DNA template is present. Zygotes for genome editing can be produced in vitro (through maturation and fertilization) or in vivo (via insemination and oviduct flushing).

CRISPR components are delivered into zygotes through microinjection or electroporation, and the resulting embryos either fresh or cryopreserved, are then transferred to recipients. This technology has diverse applications in large animals, including enhancing productivity, improving welfare and disease resistance, developing biomedical models, and controlling pest species that affect livestock.

Advantages of CRISPR in Food Production

1.      Precision and Accuracy

CRISPR allows scientists to edit specific genes with high precision. Unlike older genetic modification methods, it can target exact DNA sequences, minimizing unwanted mutations. This precision enables the development of crops and livestock with desirable traits such as improved yield, nutrition, or disease resistance—without altering other essential genes.

2.      Speed and Efficiency

Traditional breeding and genetic modification methods often take many years to produce stable traits. CRISPR drastically shortens this process, allowing researchers to achieve genetic improvements in just a few generations. This enables a rapid response to emerging agricultural challenges, such as new pests or climate-related stress.

3.      Cost-Effectiveness

CRISPR technology is simpler and cheaper compared to older genome-editing tools like TALENs and ZFNs. Its affordability opens up opportunities for smaller research institutions and developing countries to apply advanced biotechnology in agriculture.

4.      Improved Crop Yield and Quality

Through CRISPR, crops can be engineered for higher productivity, enhanced taste, longer shelf life, and increased nutritional value. For example, tomatoes have been genetically modified to produce more lycopene, rice has been improved to achieve higher yields, and wheat has been modified to improve grain quality.

5.      Enhanced Disease and Pest Resistance

CRISPR enables the creation of plants and animals resistant to viral, bacterial, and fungal infections. This reduces the need for chemical pesticides and antibiotics, lowering production costs and promoting environmental health.

6.      Tolerance to Abiotic Stress

By modifying stress-related genes, CRISPR enables crops to survive harsh conditions, including drought, salinity, and extreme temperatures. This is crucial for food security in regions vulnerable to climate change.     

 

7.      Reduced Environmental Impact

Because CRISPR edited organisms often require fewer fertilizer, pesticides, and veterinary drugs, the technology supports sustainable agriculture with less soil and water contamination.

8.      Ethical and Regulatory Advantages

Since CRISPR can create gene-edited organisms without introducing foreign DNA, many countries consider CRISPR products non-GMO. This makes them more acceptable to consumers and regulators compared to traditional genetically modified foods.

Ethical, Regulatory, and Safety Concerns

1.     Public Perception and Labelling.

The distinction between “gene-edited” and “genetically modified (GMO)” foods remains a major point of public debate. Although CRISPR often edits genes without introducing foreign DNA, many consumers still associate it with traditional GMOs. This uncertainty fuels resistance and creates a demand for transparent labelling, allowing people to make informed food choices.

2.     Ecological and Environmental Risks

Releasing CRISPR-edited crops and animals into the environment may have unintended ecological consequences. For instance, if edited species outcompete wild varieties, they could contribute to the loss of biodiversity or disrupt natural ecosystems. Continuous monitoring and ecological risk assessments are crucial for preventing long-term environmental harm.

3.     Regulatory Differences Across Region

The regulatory landscape for CRISPR foods varies widely around the world. The United States tends to classify gene-edited organisms as non-GMO if no foreign DNA is introduced, enabling faster approval. In contrast, the European Union regulates CRISPR products under strict GMO laws, requiring extensive safety evaluations. Asian countries, such as Japan and China, have adopted more flexible frameworks, but still require case-by-case reviews. These differences can complicate international trade and product commercialization.

4.      Ethical Concerns in Animal Editing

The use of CRISPR in livestock raises questions about animal welfare and the moral limits of genetic manipulation. Critics argue that even if editing improves disease resistance or productivity, it may unintentionally cause stress or alter natural behaviors. There are also concerns about patents and ownership of genetic resources, as corporations could control key traits in crops or animals, limiting access for small farmers.

Case study

A gene-edited version of edible Agaricus bisporus mushrooms

Scientists used CRISPR/Cas9 to remove a gene in the white button mushroom (Agaricus bisporus) that causes browning when the mushroom is cut. Because no foreign DNA was inserted, the USDA determined the mushroom does not require the typical GMO regulation..

Development of PRRSV-Resistant Pigs Using CRISPR-Cas9 Gene Editing

Porcine Reproductive and Respiratory Syndrome (PRRS) remains one of the most devastating viral diseases affecting global swine production. It is caused by the Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), a positive-sense RNA virus classified into two genotypes: Type 1 (European) and Type 2 (North American).

Scientists used CRISPR-Cas9 to delete a small section of the CD163 gene in pigs, blocking the entry point of the PRRS virus, which causes major economic losses in pig farming. The edited pigs became fully resistant to the virus without affecting their normal health or growth. This breakthrough demonstrates how precise gene editing can enhance animal welfare, reduce antibiotic use, and increase farm productivity, providing a sustainable solution for controlling livestock diseases.

Future Prospects and Research Directions

The future of CRISPR technology in food production looks promising and transformative. Integrating CRISPR with artificial intelligence (AI) and precision agriculture could accelerate the discovery of target genes, enabling more efficient improvements in crop and livestock production. These advances support the development of climate-smart agriculture, where gene-edited plants and animals can better withstand drought, heat, and disease pressures.

Expanding consumer acceptance through transparent communication and ethical practices will be crucial for widespread adoption. In the long term, CRISPR has the potential to build sustainable, resilient, and ethical food systems that ensure global food security while minimising environmental impact.

Conclusion

CRISPR technology has emerged as a transformative tool in modern food production, offering precise, efficient, and cost-effective solutions for improving crops and livestock. It holds the potential to enhance yield, nutrition, and resilience while reducing reliance on chemicals and minimising environmental impact.

However, its application also presents ethical, regulatory, and safety challenges that must be carefully managed. Public trust, transparent regulation, and equitable access to the technology are essential for its responsible use.

Ultimately, the future of CRISPR in agriculture depends on responsible innovation—balancing scientific progress with ethical responsibility to build a sustainable and secure food system that can feed the world's future population.

References

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