How CRISPR genome editing is changing agriculture and healthcare

Imagine if you could fix a spelling mistake in a long document with just one click. Now, imagine doing the same with the genetic code of a plant or even a human cell. That’s exactly what CRISPR-Cas genome editing allows scientists to do with remarkable precision.

In recent years, CRISPR has become one of the most talked-about breakthroughs in science of the 21st century, and has taken the scientific world by storm. Originally discovered as part of a natural defence system in bacteria, it has now evolved into a powerful tool to edit genes in plants, animals, and humans. For discovering this novel gene editing system, Emmanuelle Charpentier and Jennifer Doudna won the Nobel Prize in Chemistry in 2020.

But how does it work? Every living organism has DNA, a long string of chemical “letters” (A, T, C, G) that make up its genes, which determine everything from how we look to how plants grow. CRISPR-Cas acts as “molecular scissors” to make a cut in the DNA. Scientists programme it to locate a specific gene in an organism’s DNA (like a "GPS" to find the matching sequence of “letters” in the genome) using a guide RNA (gRNA). The gRNA and Cas protein makes a complex.

While the guide RNA binds to a specific gene (DNA sequence), the Cas protein makes a precise cut. Once that cut is made, the cell’s natural repair system takes over. In the process, scientists can delete, insert, or rewrite small parts of the genetic code. In other words, scientists can cut and edit the desired DNA at specific sites, much like a word processor allows you to edit a sentence by cutting, deleting, or changing a word.

Unlike genetically modified organisms (GMOs), which often involve inserting foreign DNA, CRISPR usually works by tweaking the organism’s own native genes. One of the most promising areas where CRISPR is making a difference is agriculture.

As farmers struggle with unpredictable weather, water shortages, pests, and declining soil fertility, scientists are turning to genome editing to create climate-resilient, high yielding, disease resistant and nutrient rich crops. India, with its vast population dependent on agriculture, is using this powerful technology for improving crops in a fast-track mode. CRISPR can also modify gut microbes in cattle to reduce methane emissions.

Transforming agriculture

Genome editing is being rapidly adopted worldwide to accelerate crop improvement. India too has launched major initiatives, notably a mega-project covering 40 crops across 34 ICAR institutes, aiming to develop high yielding, stress tolerant, disease resistant, and nutrient rich crops. In addition, there are other national level projects in progress at CSIR- and DBT-based institutes, and at other public and private sector R&D labs.

One of the most promising applications of genome editing is in reducing agriculture’s environmental footprint. For instance, reducing methane emissions from paddy fields can be achieved by developing early-maturing rice varieties. Similarly, nitrous oxide, a greenhouse gas more potent than methane or carbon dioxide, can be mitigated by engineering crops with improved nitrogen-use efficiency.

By improving traits such as water- use efficiency, photosynthetic capacity, and drought and heat tolerance, genome-edited crops offer a pathway to sustainable agriculture under climate stress. Indian researchers have recently developed two world’s first genome-edited rice varieties using CRISPR-Cas technology. The first, Pusa DST Rice 1, developed by ICAR-IARI New Delhi, is based on editing the mega variety MTU 1010 and offers strong tolerance to saline and alkaline soils. It shows up to 30% higher yields under these stress conditions.

The second, DRR Dhan 100 (Kamala), has been developed by ICAR-IIRR Hyderabad, by editing the popular Samba Mahsuri variety. It matures about 20 days earlier, yields up to 19% more, and uses water and nitrogen more efficiently leading to a reduction in greenhouse gas emissions. Both the edited varieties are devoid of foreign DNA and are treated as equivalent to conventionally bred crops under Indian regulations. Successful development of these genome-edited lines represents India’s forward leap in using precise, safe, and accelerated breeding methods to meet future food and nutrition security and climate challenges.

Boosting nutrition security

India faces significant challenges in malnutrition. For instance, protein deficiency is affecting a large proportion of the population in India. Genome editing holds great promise in enhancing the nutritional quality of staple foods. Developing protein-rich pulses, biofortified cereals, and nutrient-dense fruits and vegetables can play a critical role in addressing these deficiencies.

In addition, genome editing can aid in improving plant and soil nutrition, thereby reducing our dependence on synthetic fertilizers. One visionary goal is to engineer non-leguminous crops like cereals and oilseeds to fix atmospheric nitrogen, a biological process previously limited to legumes. Recent findings show that genome-edited plants can stimulate beneficial soil bacteria to form biofilms, opening new possibilities in atmospheric nitrogen fixation.

Beyond agriculture: Healthcare applications

Genome editing is also showing promise in healthcare, ranging from gene therapies for inherited diseases, cancer treatments, to potential cures for genetic disorders like sickle cell anaemia and thalassemia. Globally, the world's first CRISPR-based medicine, Casgevy, has already been approved in the UK, the US and the Middle East as a cure for sickle cell disease.

In a major breakthrough, the first personalized gene-edited treatment was recently administered to a child patient to treat a rare genetic disease. Research on new CRISPR-based therapies and more clinical trials are in progress globally, including India. Scientists hope that one day, it could even help in managing conditions like diabetes or heart disease by correcting defective genes.

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