In a boost to indigenous efforts at genome-edited (GE) crop breeding, Indian scientists have developed what is claimed to be a “miniature alternative” to the proprietary CRISPR-Cas proteins-based technology to precisely cut and tweak the DNA of plants.
The new GE technology — for which the Indian Council of Agricultural Research (ICAR) has recently been granted a patent — deploys the so-called TnpB or Transposon-associated proteins. These, just like the most widely used CRISPR-associated Cas9 and Cas12a proteins, act as “molecular scissors” to cleave the DNA of a gene at a predetermined target site and change its sequence. Such editing is aimed at bringing forth desirable alterations in that gene’s expression and function.
“What we have developed is a new GE system based on TnpB, instead of Cas proteins. It offers an alternative, yet highly effective next-generation tool for genome editing in plants,” said Kutubuddin Ali Molla, senior scientist at ICAR’s Central Rice Research Institute (CRRI) in Cuttack, Odisha and lead inventor of the technology.
The CRISPR-Cas technologies are controlled mainly by the Broad Institute (a partnership between the Massachusetts Institute of Technology and Harvard University) and the US seeds-cum-crop protection chemicals giant Corteva Agriscience. While Broad Institute owns the patents for CRISPR-Cas12a, Corteva has a joint licencing agreement with the former to offer access to CRISPR-Cas9 technology for agricultural applications.
While scientists have developed rice varieties using CRISPR-Cas technology, they face a major hindrance in commercial cultivation since the intellectual property (IP) rights are with global companies/institutions that may demand license fees. Here’s where indigenous genome-edited crop breeding tools will help.
The advantage with the TnpB proteins used by Dr Molla’s team is their compactness: They are much smaller, having 400-500 amino acids per molecule, compared with 1,000-1,400 for Cas9 and about 1,300 for Cas12a.
“If Cas9 and Cas12a are footballs, TnpBs are baseballs,” summed up the 40-year-old Molla, whose work has also been published in the prestigious Plant Biotechnology and highlighted in the ChemistryEurope and Nature India journals.
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The bulkiness of Cas9 and Cas12a makes it more challenging to deliver these proteins into the cells where the targeted DNA/genetic material resides. The transfer of Cas proteins is done via agrobacterium tissue culture media.
“With the hypercompact genome editor using our TnpB (which is only 408 amino acids long and sourced from an extreme environments-surviving bacteria called Deinococcus radiodurans), tissue culture-mediated delivery isn’t required. Small cargo size enables the protein to be easily packed in a viral vector that can be directly injected into the cell,” explained Molla.
GE differs from the more controversial genetic modification or GM, which involves introduction of genes from unrelated species into host plants. These could, for instance, be genes from Bacillus thuringiensis, a soil bacterium, that code for the production of proteins toxic to various insect pests in cotton.
GE entails mere “editing” of genes naturally present in the host plant, leading to mutation or changes in their DNA sequence. No foreign genes or DNA are incorporated here.
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GE has both a “molecular scissors” (whether Cas or TnpB proteins) and a so-called guide RNA that acts as a “navigator”. The latter contains a sequence that is complementary to the target DNA. It, then, guides the Cas/TnpB protein to that specific location/address in the plant genome. Once at the precise target site, the scissors make a cut in the DNA to alter or disable the particular gene.
In May 2025, the ICAR announced the release of two GE rice varieties bred by its affiliate institutions, the Hyderabad-based Indian Institute of Rice Research (IIRR) and the Indian Agricultural Research Institute (IARI) at New Delhi.
IIRR scientists used the CRISPR-Cas12a protein for editing the ‘cytokinin oxidase 2’ gene in the popular Samba Mahsuri rice variety. By reducing the expression of that gene — coding for an enzyme which regulates the number of grains produced from each plant earhead — they were able to enhance the average paddy yields of the parent variety.
IARI breeders similarly deployed the CRISPR-Cas9 protein to edit a ‘DST (drought and salt tolerance) gene’ in the MTU-1010 or Cottondora Sannalu variety. The resultant GE mutant made it possible to grow this rice even in areas prone to drought and salinity stress.
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A major issue hindering the commercial cultivation of the two GE varieties, however, is the IP rights over CRISPR-Cas technologies.
“We have been in negotiations with Corteva and Broad Institute since July 2025 and these are at an advanced stage. They have no problem with the use of their technology for academic research and breeding purposes. But when it comes to commercial planting of GE varieties derived from the same, they may insist on payment of license fees, for which we have sought waiver at least for small and marginal farmers,” a top ICAR official confirmed to The Indian Express.
That’s where the miniature alternative TnpB protein-based technology developed by Molla with his CRRI colleagues, Subhasis Karmakar and Mirza J. Baig, holds promise. “With a tool in our hand, we can do GE crop breeding freely without being bound by IP restrictions imposed from outside. It also addresses a key concern voiced by NGOs against GE technology, regarding it being controlled by foreign multinationals,” A.K. Singh, former IARI director, pointed out.
The ICAR filed the patent for the invention – titled “Systems and Methods for Targeted Genome-Editing in Plants” – on August 31, 2022. The patent for 20 years was granted by the Indian Patent Office on September 15, 2025.
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“We have also filed an international patent under the Patent Cooperation Treaty for seeking protection in other countries,” added Molla. The real test, though, would be the success in adoption of the new TnpB genome editing system by plant biotechnologists and breeders.
