Objectives of the Scheme:

1. Establishment of genome editing methods and tools, and deciphering the function of candidate genes in nutritional quality, yield and climate resilience of selected crops
2. Development of genome edited varieties with enhanced climate resilience, nutritional quality and yield of crops for ensuring sustainable, profitable and competitive food system.
3. Nurturing next generation of trained and skilled human resources in the area of genome editing for globally competitive agriculture.

Background of the Scheme:

By 2047 we need to produce 520 million tonnes of food grains, which 1.6 times ofwhat we produce today. Further, we need to increase the efficiency of water and nutrientuse efficiency by >1.7 fold. This is a major challenge to agriculture due to dwindlingfresh water resources, deteriorating soil health and climate change. Besides reducing theproductivity, climate change also reduces the quality of the food grains. Currentproduction of pulses is about 24 million tonnes which needs to be increased by 33% by2030. Similarly, domestic production of edible oil is only one-third of the demand today,and by 2030, expected demand for vegetable oils is 34 million tonnes.

Thus, for food andnutritional security and achieve sustainable development goals, a quantum jump in yieldand quality is necessary. This increase must come mainly from the improved genetic gain in crop improvement programs.Genetic variation induced by spontaneous or induced mutation is the fundamentalfor genetic improvement of plants/animals.

Induced mutations are extensively used ingenetic improvement of crops. However, mutations induced by physical and chemicalmutagens are random and unpredictable, and often difficult to get desirable mutation withimproved economic traits. Further, transfer of desirable mutant from one geneticbackground to another genetic background through breeding program is time and labourintensive, and often undesirable character associated with the mutant is also transferredto the newly developed variety. Hence scientists were looking for precision mutagenesismethods which can be used to create desirable mutations in any gene.

Genome editing is biological mutagenic tool to precisely create mutations in thegenome of an organism for obtaining desirable traits or repair of genetic defects in anorganism. The CRISPR-Cas (Clustered Regularly Interspaced Short PalindromicRepeats/CRISPR-associated protein) method of genome editing for creation of mutationsin the genome of plants, animals and microorganisms with extremely high precision wasdiscovered in 2012 by Emmanuelle Charpentier and Jennifer A. Doudna. They wereawarded with the Nobel Prize in Chemistry in 2020, as within the very short period oftime this technology has revolutionised agriculture and medicine.

The CRISPR-Cas technology has two components: 1) ~ 20 nucleotide long guideRNA (gRNA) and 2) Cas enzyme, the molecular scissors. Once the gRNA and Casenzyme are delivered in to a cell, the gRNA takes the Cas enzyme to the target location, where the Cas enzyme cut in the DNA to make DNA double strand break(DBS). This DNA DSB is repaired by the natural cellular DNA repair enzymes. Duringthis repair process, errors caused by native enzymes lead to addition or deletion of fewnucleotides.

This type of mutation is called Site Directed Nuclease 1 (SDN 1) mutation.When an exogenous repair DNA template (same as native DNA except for few alphabetschange in the gene sequence) is provided to the cell, the DNA is integrated in to brokensite, and thus very precisely few nucleotides can be substituted. This type of mutation iscalled Site Directed Nuclease 2 (SDN 2) mutation. When a foreign DNA is provided asrepair template, foreign genes can be precisely inserted in the safe harbour loci in thegenome. This type of mutation is called Site Directed Nuclease 3 (SDN 3) mutation.

Inthe first generation of mutants, the plant will have the transgene (gRNA, Cas9 andselection marker gene), and the desirable mutation. In the second generation, plants withthe desired mutant is segregated from the transgene. Thus, mutants developed by SDN1and SDN2 methods of genome editing are indistinguishable from natural/inducedmutants, free from transgene, and thus are non-GM (non-Genetically Modified) plants.SDN3 mutants are similar to the GM plants. Genome editing has emerged as New Breeding Technology (NBT) to instantlycorrect the genetic defects in elite popular cultivars and improve them in a shorter timeas compared with that required under conventional breeding and marker assistedbreeding. Further, Genome editing in wild or related plant species to enable theirdomestication suitability by cultivation through elimination unwanted genomic regionsor correcting deleterious/toxic/expression limiting alleles/genes/ for adding to food/feedor industrial use diversification of agrobiodiversityThe CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9-mediated genome editing has emerged as new breeding technology.

Globally severalcountries are intensively working on development of products using gene editing. Until2020, about 231 market-oriented products in agriculture using gene editing have beenpublished. USA has given non-regulated status to 168 genome edited products. During2015 to 2020, transgene-free genome edited crops have been given non-regulated statusin countries viz., U.S.A, Australia, Japan, Argentina, Brazil, Colombia, Chile,Guatemala, Honduras, Paraguay, Israel and Nigeria. India has also exempted transgenefree genome edited lines developed by SDN1 and SDN2 approaches from the Rules 1989.

The Calyxt soybean, with “high oleic” oil with no trans-fats and less saturated fat,developed by genome editing is commercially cultivated from 2018 and the oil is sold inthe market of USA from 2019. Currently it occupies 40000 ha. Similarly, herbicidetolerant canola developed by CRISPR-Cas method was declared as Non-GM and iscultivated from 2017 in both USA and Canada. In 2021, Japan has permitted genomeedited tomato with high levels of gamma-aminobutyric acid (GABA which help lowerblood pressure), for commercial cultivation as non-GMO. Already genome edited canolain USA, and tomato and fishes (Tiger puffer, Red sea bream) in Japan are marketed forconsumption.

Making of genome edited crops free from GM regulation is a key step forharnessing this powerful technology. Towards this, Ministry of Environment, Forest andClimate Change (MoEF & CC) has issued an Office Memorandum (O.M.) regarding theexemption of specified categories of genome edited plants from the provisions of Rules7 to 11 (both inclusive) of the “Rules for the manufacture, use, import, export & storageof hazardous microorganisms/genetically engineered organisms or cells,1989” (Rules,1989) of the Environment (Protection) Act, 1986. This exemption applies to site-directednuclease (SDN)-1 and SDN-2 categories of genome edited plants, which are free fromexogenous introduced DNA.

Copy of the O.M. F. No. C -12013/3/2020-CS-III dated 30thMarch 2022. Pursuant to the O.M., Department of Biotechnology (DBT), Ministry ofScience and Technology notified the ‘Guidelines for the Safety Assessment of GenomeEdited Plants, 2022’ on 17th May 2022 for research and development of genome editedplants in India. SOPs for regulatory review of genome edited plants under SDN-1 andSDN-2 categories, 2022 have been released by DBT vide File No. PID-15011/2022/PPBDBTdated 04.10.2022. It was decided that all the science departments should take-upthe research activities for development of genome edited products..

In ICAR, under the NASF funded project, genome editing was successfully utilisedto develop high yielding, drought and salt tolerant mutants in mega rice cv. MTU1010,and high yielding mutant of rice cv. Samba Mahsuri, at IARI New Delhi, and IIRRHyderabad, respectively. We have obtained IBSC and RCGM exemption for thesemutants from Rules 7-11 of Rules 1989, and for the first time in the Country, genomeedited mutants have been nominated to AICRIP trails in kharif 2023.

These mutants areexpected to be released in 2024. Further under this project, at ICGEB New Delhi, geneedited mutants of DEB1, CKX2 and TB1 were developed in the rice cv. MTU1010, andthese mutants are now being analysed for identification of exogenous introduced DNAfree lines, and are expected to enter field trials in kharif 2024. Similarly, NRRI Cuttackhas developed IPA1 edited lines of Swarna, and these mutants are now being analysedfor identification of exogenous introduced DNA free lines, and are expected to enter fieldtrials in kharif 2024.

For globally competitive agriculture deployment of genome editing technologiesareessential as improved varieties with yield, nutritional quality and climate resiliencewith less agrochemical requirements can be developed and deployed in a cost-effectivemanner. The Indian Council of Agricultural Research proposes a project on “Enhancingclimate resilience and ensuring food security with genome editing tools” for fasttrackingthe development crop varieties with improved yield, nutritional quality andclimate resilience by using genome editing.