BIOTECHNOLOGY. Reaping benefits: ‘Scissors’ snip off bad genes in plants

Move over controversial transgenic crops. Plant breeders now have a genome editing technology for vastly improved crop varieties.

Gene (genome) editing techniques, being developed from the 1990s, stayed largely out of the limelight until a pair of “molecular scissors” called CRISPR-Cas9 was discovered by two women biologists in 2012. Emmanuelle Charpentier of France and Jennifer Doudna of the US won the Nobel Prize for Chemistry in 2020 for this.

Unlike transgenic technology, in which genes from other organisms are inserted for developing better crops, the CRISPR-Cas9 technique makes it possible to add, remove or alter genetic material so as to add a beneficial trait or remove a deleterious one. It is largely considered safe as no foreign genes are used to alter the plant genome in most cases.

CRISPR-Cas9 can modify genetic material in the genome, like other gene editing tools such as zing finger nucleases and Transcription activator-like effector nuclease. The difference is that the new method, adapted from a naturally occurring gene editing system in bacteria, does the job more accurately and efficiently, and is cheaper and faster.

The technology will help scientists develop new disease-resistant and high-yielding varieties in a matter of weeks rather than a couple of years taken otherwise. The US has already released dozens of crops for production, while hundred others are still in labs. In 2016, Dupont Pioneer, which later merged with Dow Chemical Company, engineered a maize variety which produces amylopectin — a sugar-like molecule used in processed foods, adhesives and high-gloss paper — by knocking out a gene coding for another starch called amylose. Low-nicotine tobacco, anti-browning mushrooms and fragrant moss for homes have also been developed.

No crop has yet been released for commercial cultivation in China, but editing tools are being trained on rice, wheat, vegetables and fruits.

Gene editing tools, collectively called Site-Directed Nucleases (SDN) technology, identify a specific target sequence of DNA and cut the DNA at that location. For instance, with CRISPR-Cas9, researchers create a small piece of RNA with a short ‘guide’ sequence that binds to a specific location on the genome. The Cas9 enzyme, also attached to the same RNA, works like scissors to create a cut in the DNA. Once the DNA is cut, the researchers have three options available to them.

First, in what is called SDN-1, scientists use the cell’s own repairing machinery to mend short insertions and deletions made to the existing genetic material. For the second (SDN-2), they insert an additional DNA repair template for additions or deletions at the site to activate the desired trait. No foreign gene is used in either of these approaches. The third method (SDN-3) uses a gene from a related or unrelated species or even a synthetic gene.

India is still in the process of deciding whether to allow gene editing for better crops. “Indian scientists have been arguing that since SDN-1 and SDN-2 do not use any foreign gene, the crops developed using these methods should be treated as normal crops. Those developed using SDN-3 can be placed under GMO regulation,” says Chinnusamy Vishwanathan, Principal Scientist and Head of Department of Plant Physiology, Indian Agricultural Research Institute, Delhi.

Many research groups, however, are already trying to use genome editing tools for crop improvement. Vishwanathan is using gene editing to introduce salt tolerance (which helps a crop grow in saline water) in a popular rice variety, MTU1010, grown over 3 million hectares in eastern and southern India.

MK Reddy, a scientist at the International Centre for Genetic Engineering and Biotechnology, Delhi, has been working in this field, too. “Too many years of cultivation have led to accumulation of too many negative genes in the rice plant.” Reddy cites the example of genes that inhibit tillering (or branching) of rice. “If I knock out those genes, I would get more tillering,” he says.

Gene editing can also help improve a plant’s innate immunity. When pathogens such as fungi invade a plant system, they inactivate its innate immunity to survive inside the plant. This can be tackled with technology, Reddy adds.

Further, a generation down the line, these plants do not show signs of editing. “Whatever tools I put to edit the genome are removed in the next generation crop,” he explains.

Most scientists in the field of biotechnology feel that gene editing can solve problems of decreasing agricultural productivity and loss of arable land as well as issues triggered by climate change in food production.

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