Written by Venkata Sresty Tavva, Shaibal Dasgupta | New Delhi | Updated: January 30, 2020 5:04:50 am

Increased agricultural production and sustainable food security is of paramount importance for a growing population, both globally and in India. Rice is one of the major staple food crops, on which over half of the worlds population and 80% of Asians are dependent for meeting their daily energy needs. India is the second largest consumer (around 100 million tonnes) as well as producer (115 million tonnes) of milled rice after China.

Rice, like other crops, is exposed to various biotic and abiotic stresses during its life cycle. Several diseases such as bacterial leaf blight and blast, and insect pests like the brown plant hopper, cause significant damage that result in devastating yield reductions. The crop losses from some of these biotic stresses can be as high as 50% and even reach 90% in epidemic conditions. In addition, rice accounts for more than half of the fresh water used in agriculture. Water availability for agriculture in general is becoming a significant constraint now, due to ever-increasing domestic, urban and industrial consumption requirements. The situation will become more complex with decreased arable land availability as well, not to speak of the impact of climate change on crop productivity.

Successful development of rice lines, incorporating important biotic and abiotic stress resistant traits, can provide solutions for minimising yield losses that affect consumers (from reduced availability) and producers (from lower incomes) alike. This may, however, require adoption of innovative technologies, as the existing breeding techniques based on physical crossing of parental plants may not be enough. One such approach is targeted genome editing of crop plants, which could yield varieties with desired traits within a short period of time compared to traditional breeding methods. For this, we must first identify rice varieties that are already being grown extensively in a selected geography and develop strategies for improving traits such as disease and pest resistance, drought tolerance, etc.

In the last six years, targeted genome editing using CRISPR/Cas9 has captivated the attention of the research community. The applications of this technology an acronym for clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 have gained significant traction in various fields of science, including agriculture.

CRISPR/Cas9 was originally identified and adapted from a naturally-occurring immunity mechanism in bacteria, which is employed against invading viruses. The bacteria basically capture snippets of DNA from the viruses and use them to create CRISPR arrays. These DNA segments allow the bacteria to remember the viruses. In the event of the viruses attacking, the bacteria produce RNA (messenger that carries genetic information from the DNA) from the CRISPR arrays. The bacteria then uses Cas9 enzyme, which acts as a pair of molecular scissors, to cut the DNA apart and disabling the virus.

The same system has been engineered by researchers to produce RNA complementary to a specific target DNA sequence in the genome of an organism. This guide RNA binds itself only to that target sequence and no other regions of the genome. The Cas9 enzyme will, in turn, follow the guide RNA and cut the two strands of DNA at the targeted location. At this stage, the cell knows that the DNA is damaged and tries to repair it. The researchers can now use the natural DNA repair machinery to introduce changes, including by adding or deleting genetic material.

Such genome editing using CRISPR/Cas9 is possible through three different approaches: Site-Directed Nuclease (SDN) 1, 2 and 3. SDN1 produces a double-stranded break in the genome of a plant and modifies an existing trait without undertaking insertion of any foreign DNA or even editing at the site of interest. SDN2 modifies the trait of interest by producing a double-stranded break and, while that is being repaired by the cell, editing a small sequence at the target site. SDN3 uses site-specific insertion of a large, foreign DNA fragment to introduce a new trait of interest.

In the case of SDN1 and SDN2 approaches, the CRISPR components used to edit the selected native genes for a desirable trait can easily be removed by segregation of the plant progeny in the next and subsequent generations. In this way, one can produce transgene-free edited plants (in other words, non genetically-modified or non-GMOs) that are indistinguishable from conventional breeding material. But this method is faster and cheaper than traditional crossing, which results in a host of unwanted traits also getting transferred and, hence, requires several more breeding cycles in order for the offspring to have only the desired traits. The use of CRISPR/Cas9 technology has been successfully demonstrated, for instance, in developing rice lines that are resistant to blast (by knocking-out genes that suppress immunity to the fungus) and bacterial leaf blight (by editing the binding sites of the disease-causing genes).

Globally, regulatory policies for genome edited crops, as opposed to transgenic or GMOs, are in different stages of implementation. Countries with available regulatory processes for genome edited lines include the United States, Canada, Argentina, Israel, Chile, Brazil, Australia and Japan. Regulatory agencies in India are still deliberating over the extent of regulation required for crop plants developed through gene editing, which does not involve addition of DNA from totally unrelated species.

When it comes to new gene editing technologies, we need rational analyses of the risks and benefits that the technology offers in each scenario; we need to strengthen our research efforts in scientific technologies that offer the most benefit to society through strategic funding, collaborations or even public-private partnerships; and we need clear regulatory frameworks for the application of these technologies. Every step we take could help reduce hunger and improve the quality of life for ourselves and future generations.

The writers are Group Leaders at Tata Institute for Genetics and Society, Bengaluru

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