India Develops TnpB Genome Editing Tool: Indigenous Alternative to CRISPR for Next-Gen Crop Improvement

• India has taken a major leap toward building its own genome-editing ecosystem as the Indian Council of Agricultural Research (ICAR) has secured a patent for a breakthrough editing platform based on Transposon-Associated Protein B (TnpB).
• This advancement is crucial because it offers an indigenous alternative to the globally patented CRISPR-Cas9 and CRISPR-Cas12a systems, which remain under strict IP control of institutions like the Broad Institute (MIT–Harvard) and Corteva Agriscience.
• For a country where crop improvement—high yield, resilience to climate stress, and better disease tolerance—is a national priority, a home-grown genome-editing tool eliminates licensing challenges and opens doors for affordable and large-scale innovation.

Understanding Transposons and the Role of TnpB

• To appreciate ICAR’s achievement, one must understand transposons, often described as “jumping genes” because they move from one location to another within the genome.
  • These mobile genetic elements often carry associated proteins, and one such protein is TnpB.
• TnpB works like a molecular scissor, enabling scientists to cut DNA precisely at pre-selected sites. After the DNA is cut, TnpB can facilitate gene editing, gene modification, or gene silencing.
• Its mechanism closely resembles the function of CRISPR-associated enzymes like Cas9 and Cas12a, which led the global genome-editing revolution.
• However, TnpB has a major advantage:
  • TnpB is extremely compact—only 400–500 amino acids
  • Cas9 typically ranges from 1,000–1,400 amino acids
  • Cas12a is about 1,300 amino acids
• This compactness makes TnpB easier to deliver into plant cells, and crucially, it can fit inside delivery vehicles like viral vectors. This reduces dependency on complicated tissue-culture methods typically needed for CRISPR-based editing.

Why TnpB Is a Key Breakthrough for Indian Crop Science

• According to Dr. Kutubuddin Ali Molla, senior scientist at ICAR-CRRI (Cuttack) and the lead innovator, TnpB is essentially a “miniature CRISPR alternative”.
  • Its small size significantly improves delivery efficiency, especially when sourced from Deinococcus radiodurans, a bacteria species known for extraordinary survival in extreme conditions.
• This makes TnpB-based genome editing not only powerful but also highly workable for routine crop-breeding programs.

Genome Editing (GE) vs Genetic Modification (GM)

India’s regulatory and scientific community has repeatedly emphasized the difference:

• Genetic Modification (GM) inserts foreign genes from unrelated organisms (e.g., Bt cotton).
• Genome Editing (GE) edits the plant’s existing genes without adding external DNA.

GE requires two essential components:

1. DNA-cutting proteins — Cas9, Cas12a, or TnpB
2. Guide RNA (gRNA) — directs the protein to the specific target gene

India’s Advancements in Genome-Edited Crops

India already demonstrated successful use of GE tools by releasing two genome-edited rice lines in May 2025:

• IIRR Hyderabad used CRISPR-Cas12a to modify the cytokinin oxidase 2 gene in Samba Mahsuri, boosting grain yield.
• IARI New Delhi applied CRISPR-Cas9 to edit the DST gene in MTU-1010, enabling cultivation in drought- and salinity-prone regions.

However, commercialization is complicated because CRISPR is governed by international patents. Even if Indian scientists develop a GE crop, the seed’s commercial release may still require paying licensing fees to foreign patent holders.

This is exactly where ICAR’s TnpB innovation becomes transformative:

• It is fully indigenous
•  Protected by Indian patent law
• Free from foreign IP licensing

ICAR’s Patent and International Protection

• ICAR filed its application titled “Systems and Methods for Targeted Genome Editing in Plants” on 31 August 2022.
  The Indian Patent Office granted a 20-year patent on 15 September 2025.
• To protect global commercialization, ICAR has also submitted an international patent under the Patent Cooperation Treaty (PCT).

The Parallel Rise of the enFnCas9 Platform in India

• Alongside TnpB, India is strengthening other genome-editing tools.
  A major collaboration between CSIR-IGIB and the Serum Institute of India aims to scale affordable therapies using enFnCas9, an engineered, high-fidelity variant of Francisella novicida Cas9.
• This CRISPR platform offers fewer off-target edits and may become a key technology in future gene therapies for Indian patients.

A New Phase for India’s Indigenous Biotechnology Efforts

• The compact, efficient, and easily deployable TnpB system positions India at the forefront of a new era in agricultural biotechnology.
• It enhances national scientific autonomy, reduces reliance on foreign patents, speeds up genome-edited crop development, and counters concerns about multinational monopolies in seed biotechnology.
• The next crucial step lies in widespread adoption by plant breeders, research institutions, and biotech innovators. If embraced at scale, TnpB could catalyze a sovereign, sustainable, and widely accessible genome-editing ecosystem for India’s agriculture sector.