TnpB vs CRISPR: India Launches Its Own Genome Editing Technology for Crop Improvement
- TPP
- Nov 21
- 3 min read
Why TnpB Matters: Compact Gene Editing Tool Developed by ICAR to Replace CRISPR in GE Crops
India has taken a major step toward indigenous genome-editing capability with the Indian Council of Agricultural Research (ICAR) securing a patent for a new genome-editing system based on Transposon-Associated Proteins (TnpB).
This breakthrough is particularly significant because it offers a home-grown alternative to the widely used but IP-restricted CRISPR-Cas9/Cas12a technologies, which are controlled by global institutions such as the Broad Institute (MIT–Harvard) and Corteva Agriscience.
For Indian agriculture—especially the development of high-yield, stress-tolerant and disease-resistant crops—an indigenous tool removes licensing burdens and opens the door to more affordable innovation.
What Are Transposons and TnpB?
To understand this development, it is essential to know that transposons, also known as “jumping genes”, are DNA segments capable of moving from one position to another within a genome. These movements occur within a single cell and often bring with them associated proteins. One such protein is TnpB (Transposon-associated Protein B).
TnpB functions like a molecular scissor, meaning it can cut DNA at predetermined locations. Once the DNA is cut, TnpB can help edit, modify, or silence specific genes.
This mechanism is similar to CRISPR-associated proteins like Cas9 and Cas12a, which popularized the modern genome-editing revolution. However, what makes TnpB especially attractive is its compact size—TnpB proteins consist of 400–500 amino acids, nearly half the size of Cas9 (1,000–1,400 amino acids) and Cas12a (~1,300 amino acids).
A smaller protein is easier to deliver into plant cells and can be packaged inside viral vectors, eliminating the need for complex tissue-culture based delivery methods.
Why TnpB Matters for Indian Agriculture
According to Dr. Kutubuddin Ali Molla, senior scientist at ICAR-CRRI (Cuttack) and lead inventor, TnpB acts as a “miniature alternative” to CRISPR-Cas systems. Its compactness significantly simplifies delivery into plant cells—especially when sourced from Deinococcus radiodurans, a bacterium famous for surviving extreme environments. This makes TnpB-based genome editing not only efficient but also more accessible for routine crop-breeding purposes.
Genome Editing (GE) is fundamentally different from Genetic Modification (GM).
GM involves inserting foreign genes from unrelated species (e.g., Bt genes in cotton).
GE, on the other hand, involves editing genes already present within the plant itself—no external DNA is introduced.
GE uses two key components:
Molecular Scissors – Cas9, Cas12a, or TnpB proteins that cut DNA.
Guide RNA (gRNA) – A short RNA sequence that directs the scissors to the exact location of the target gene.
India’s Progress in Genome-Edited Crops
India has already released two GE rice varieties (May 2025), showcasing the practical potential of genome editing:
Hyderabad’s Indian Institute of Rice Research (IIRR) used CRISPR-Cas12a to edit the cytokinin oxidase 2 gene in Samba Mahsuri, increasing grain yield.
IARI New Delhi used CRISPR-Cas9 to modify the DST (drought and salt tolerance) gene in MTU-1010, enabling the variety to grow in drought and salinity-prone regions.
However, the commercial cultivation of these varieties faces hurdles due to intellectual property restrictions on CRISPR tools. Global patent holders may demand license fees for commercial seed release—even if Indian institutions developed the varieties.
This is where TnpB technology becomes a game-changer:It is indigenous, patented in India, and free from foreign licensing barriers.
The ICAR Patent and Global Protection
ICAR filed its patent, titled “Systems and Methods for Targeted Genome Editing in Plants”, on 31 August 2022, and it was granted a 20-year patent on 15 September 2025 by the Indian Patent Office. Additionally, ICAR has filed for an international patent under the Patent Cooperation Treaty (PCT) to secure global rights and commercial protection.
Relevance of the enFnCas9 Platform
Parallel to TnpB, India is also strengthening other genome-editing systems. An agreement between CSIR-IGIB and the Serum Institute of India aims to scale affordable therapies using the enFnCas9 platform—an engineered Francisella novicida Cas9 variant.
This high-fidelity CRISPR system offers fewer off-target effects and is being positioned as another indigenous alternative for genetic disorder therapies.
A New Era for Indigenous Genome Editing
With the compact, efficient, and easily deliverable TnpB-based genome editing system, India now stands at the brink of a new biotechnology era.
The tool strengthens national self-reliance, reduces dependence on foreign patents, accelerates GE-crop development, and addresses concerns raised by NGOs over multinational dominance in agricultural biotechnology.
The real test ahead lies in adoption by plant breeders and biotechnology institutions. If widely embraced, TnpB could lay the foundation for a truly sovereign and scalable genome-editing ecosystem in India.