Demystifying Genome Editing. Scissors of science: Genome editing shapes the future of farming

India has made a significant leap on the technology continuum with the recent approval of genome-edited rice varieties. Hailed as the world’s first, these rice varieties are set to stir the scientific world, as countries increasingly adopt breakthrough genome-editing technologies to accelerate sustainable rice production and remain competitive in international trade.

Rice, often referred to as the “staff of life” holds deep cultural and traditional significance across the globe. It binds commerce and culture and provides essential calories to humanity. In this context, the approval of the world’s first genome-edited rice varieties is a landmark step that promises food security for the poorest of the poor in the years to come.

At the same time, the development has ignited debates around the nature and usefulness of the technology, particularly on social media, where concerns have surfaced about the safety of genome editing in a staple crop like rice. Addressing these public concerns in simple language by demystifying the nuances and technicalities is vital for improving public understanding. It also provides crucial insight for framing informed policy decisions on genome editing in rice and other important crops. Simplifying the complexity of genome editing is essential to prevent misunderstandings and counter misinformation propagated by certain interest groups that have recently raised concerns over the safety of genome-edited rice and its impact on India’s rich biodiversity.

India’s pioneering move to approve genome-edited rice should serve as a case study in responsible biotech innovation. A helpful way to explain genome editing to the layperson is by comparing it to tailoring. This analogy likening CRISPR-Cas genome editing to a tailor using scissors to alter fabric, helps simplify a complex concept and invites broader public engagement with one of the most transformative technologies of our time.

CRISPR-Cas genome editing: The genetic tailor

Imagine a master tailor seated before a long stretch of fabric (Figure 1). The master tailor carefully inspects every inch to draw a specific pattern or find imperfections or areas that need alteration. Using chalk, the tailor marks specific spots before picking up sharp scissors to make precise cuts. In this analogy, the tailor represents a scientist or researcher using the CRISPR-Cas system.

Figure 1. CRISPR-Cas Genome Editing as a Tailor Using Scissors

The fabric is the genome (DNA)

Now, shift your imagination from the world of fabric to the complex code of life DNA or deoxyribonucleic acid, which is the hereditary material in all known living organisms, including human, animal and plants. It is composed of long sequences of nucleotides - the building blocks that form genes. These genes determine everything from the shape, size and colour of the fruits to risk for certain diseases in plants or vulnerability to climatic adversities. In our analogy, think of DNA as a roll of fabric which can be fashioned into different garments. Similarly, DNA can be expressed in various ways to create the diversity of life in plant, human and animal. But like fabric, DNA isn’t immune to errors. Sometimes the weave is off. A pattern doesn’t come out right. That’s where genetic tailoring comes into play.

This “genetic tailoring” is exactly what scientists in India have recently achieved with new rice varieties like DRR Dhan 100 (Kamla) and Pusa Rice DST 1. Using CRISPR-Cas, the tailor’s precise tools, scientists of IARI and IIRR have skilfully “altered the fabric,” in this case the DNA of rice to create improved versions of Sambha Mahsuri and MTU1010 rice variety, respectively. For instance, IIRR scientists uses CRISPR-Cas technique to “knock out” a tiny genetic piece of OsCKX2, a gene in rice that encodes a cytokinin oxidase enzyme involved in the degradation of cytokinin in the rice plant. By disabling the OsCKX2 gene, the plant accumulates more cytokinin in the panicle tissue, promoting the development of more grains and earlier maturity.

The tailor’s toolkit: CRISPR-Cas plasmid

In traditional tailoring, the tailor uses a pattern or chalk outline to know exactly where to cut. They then use a pair of scissors to make the precise incisions necessary for alterations. Similarly, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) plasmid includes tools for Cas9 expression, guide RNA cloning and various CRISPR-based applications such as knockout, suppression or activation etc. CRISPR plasmid is a system that uses a guide RNA to find a specific spot in the plant genome DNA and a Cas9 protein to make a cut. An analogy of different components of CRISPR-Cas genome editing as a tailor ‘s toolkits is illustrated in the table 1.

Table 1. Comparing Genome Editing Tools to Tailoring Toolkit

The custom pattern is the guide RNA (gRNA)

Before making any cuts, the tailor uses a very specific pattern or mark. This pattern is meticulously designed to match only one exact spot on the fabric where a change is needed. This pattern is akin to guide RNA (gRNA) in CRISPR. The gRNA is a custom-designed molecule to find and bind to a very precise gene sequence, such as the sequence of the targeted rice gene OsCKX2 within the vast rice DNA.

The scissors are the Cas Protein (Cas9)

The Cas9 protein is the tailor’s scissors that follow that specific pattern or mark and make a clean cut at the right location. Just as a good tailor avoids cutting too much or too little, scientists using CRISPR-Cas9 ensure that edits occur only at the intended site, in this case the location of OsCKX2 gene, preserving the overall integrity of the DNA strand.

The cutting spot: PAM sequence

Sometimes, the tailor’s scissors require a specific notch or marker to begin the cut. In genome editing, this corresponds to the Protospacer Adjacent Motif (PAM) - a short, specific DNA sequence that the Cas9 protein must recognise before making its incision near the target gene. The PAM acts as a necessary checkpoint before editing the OsCKX2 gene.

Making the alteration: Genome editing in action

Once a tailor makes a cut in the fabric, they have multiple options. They can remove a flawed piece, patch in new material or even stitch parts together in a new configuration. Likewise, after Cas9 cuts the DNA, the cell’s natural repair mechanisms take over. Scientists can exploit this moment of repair to introduce desired changes such as correcting mutations, inserting new genes expressing high oleic or herbicide tolerant gene or disabling harmful ones like OsCKX2 gene in rice.

The final product: Improved rice varieties

The tailoring analogy underscores precision and customisation. A master tailor works with intention and care, and so does CRISPR-Cas. Unlike older genetic modification methods, which could introduce foreign genes haphazardly, CRISPR-Cas allows scientists to make targeted edits without altering surrounding DNA. The result is enhanced rice varieties that are more productive, resilient and better suited for challenging climates, all without incorporating foreign DNA from unrelated species that might jeopardise international rice trade.

India plays a pivotal role in the global rice market. It exported nearly 16.4 million tonnes of both basmati and non-basmati rice in 2023–24, valued at approximately $10.4 billion. Alongside other leading exporters such as Thailand, Vietnam, Pakistan and the United States, India significantly influences global supply chains. Looking ahead, as India advances in genome-edited breakthroughs in rice cultivation to enhance domestic production and contribute a record-breaking 24 million tonnes to the global rice trade, projected at 59.7 million tonnes by 2025-26.

The future of genetic tailoring

This precise “genetic tailoring” of plant genomes addresses critical challenges in food security and sustainability, much like how well-crafted clothing meets both function and comfort. Yet, as with tailoring, precision matters. A misstep could spoil the entire piece. Similarly, any misuse or unintended effects of genome editing such as off-target mutations that could have serious implications.

That’s why ethical considerations, regulatory oversight, and strict scientific protocols such as the guidelines for genome-edited plants and the standard operating protocols (SOPs) for genome-edited plants, jointly developed by the Department of Biotechnology (DBT) and the Ministry of Environment, Forest and Climate Change (MoEF&CC) are essential to guide the safe and responsible use of genome editing in agriculture.

The authors represent South Asia Biotechnology Centre (SABC), Jodhpur

Published on May 25, 2025