ICAR EFC - Enhancing climate resilience and ensuring food security with Genome Editing Tools.

Objectives of the Scheme

• Establishment of genome editing methods and tools, and deciphering the function of candidate genes in nutritional quality, yield and climate resilience of selected crops.
• Development of genome edited varieties with enhanced climate resilience, nutritional quality and yield of crops for ensuring sustainable, profitable and competitive food system.
• 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 of what we produce today. Further, we need to increase the efficiency of water and nutrient use efficiency by >1.7 fold. This is a major challenge to agriculture due to dwindling fresh water resources, deteriorating soil health and climate change. Besides reducing the productivity, climate change also reduces the quality of the food grains. Current production of pulses is about 24 million tonnes which needs to be increased by 33% by 2030. 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 and nutritional security and achieve sustainable development goals, a quantum jump in yield and 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 fundamental for genetic improvement of plants/animals. Induced mutations are extensively used in genetic improvement of crops. However, mutations induced by physical and chemical mutagens are random and unpredictable, and often difficult to get desirable mutation with improved economic traits. Further, transfer of desirable mutant from one genetic background to another genetic background through breeding program is time and labour intensive, and often undesirable character associated with the mutant is also transferred to the newly developed variety. Hence scientists were looking for precision mutagenesis methods which can be used to create desirable mutations in any gene.

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

The CRISPR-Cas technology has two components: 1) ~ 20 nucleotide long guide RNA (gRNA) and 2) Cas enzyme, the molecular scissors. Once the gRNA and Cas enzyme 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. During this repair process, errors caused by native enzymes lead to addition or deletion of few nucleotides. 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 alphabets change in the gene sequence) is provided to the cell, the DNA is integrated in to broken site, and thus very precisely few nucleotides can be substituted. This type of mutation is called Site Directed Nuclease 2 (SDN 2) mutation. When a foreign DNA is provided as repair template, foreign genes can be precisely inserted in the safe harbour loci in the genome. This type of mutation is called Site Directed Nuclease 3 (SDN 3) mutation.

In the first generation of mutants, the plant will have the transgene (gRNA, Cas9 and selection marker gene), and the desirable mutation. In the second generation, plants with the desired mutant is segregated from the transgene. Thus, mutants developed by SDN1 and SDN2 methods of genome editing are indistinguishable from natural/induced mutants, 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 instantly correct the genetic defects in elite popular cultivars and improve them in a shorter time as compared with that required under conventional breeding and marker assisted breeding. Further, Genome editing in wild or related plant species to enable their domestication suitability by cultivation through elimination unwanted genomic regions or correcting deleterious/toxic/expression limiting alleles/genes/ for adding to food/feed or industrial use diversification of agrobiodiversity. The CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9-mediated genome editing has emerged as new breeding technology.

Globally several countries are intensively working on development of products using gene editing. Until 2020, about 231 market-oriented products in agriculture using gene editing have been published. USA has given non-regulated status to 168 genome edited products. During 2015 to 2020, transgene-free genome edited crops have been given non-regulated status in countries viz., U.S.A, Australia, Japan, Argentina, Brazil, Colombia, Chile, Guatemala, Honduras, Paraguay, Israel and Nigeria. India has also exempted transgene free 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 in the market of USA from 2019. Currently it occupies 40000 ha. Similarly, herbicide tolerant canola developed by CRISPR-Cas method was declared as Non-GM and is cultivated from 2017 in both USA and Canada. In 2021, Japan has permitted genome edited tomato with high levels of gamma-aminobutyric acid (GABA which help lower blood pressure), for commercial cultivation as non-GMO. Already genome edited canola in USA, and tomato and fishes (Tiger puffer, Red sea bream) in Japan are marketed for consumption.

Making of genome edited crops free from GM regulation is a key step for harnessing this powerful technology. Towards this, Ministry of Environment, Forest and Climate Change (MoEF & CC) has issued an Office Memorandum (O.M.) regarding the exemption of specified categories of genome edited plants from the provisions of Rules 7 to 11 (both inclusive) of the “Rules for the manufacture, use, import, export & storage of hazardous microorganisms/genetically engineered organisms or cells,1989” (Rules, 1989) of the Environment (Protection) Act, 1986. This exemption applies to site-directed nuclease (SDN)-1 and SDN-2 categories of genome edited plants, which are free from exogenous introduced DNA. Copy of the O.M. F. No. C -12013/3/2020-CS-III dated 30th March 2022. Pursuant to the O.M., Department of Biotechnology (DBT), Ministry of Science and Technology notified the ‘Guidelines for the Safety Assessment of Genome Edited Plants, 2022’ on 17th May 2022 for research and development of genome edited plants in India. SOPs for regulatory review of genome edited plants under SDN-1 and SDN-2 categories, 2022 have been released by DBT vide File No. PID-15011/2022/PPB-DBT dated 04.10.2022. It was decided that all the science departments should take-up the research activities for development of genome edited products.

In ICAR, under the NASF funded project, genome editing was successfully utilised to 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 IIRR Hyderabad, respectively. We have obtained IBSC and RCGM exemption for these mutants from Rules 7-11 of Rules 1989, and for the first time in the Country, genome edited mutants have been nominated to AICRIP trails in kharif 2023. These mutants are expected to be released in 2024. Further under this project, at ICGEB New Delhi, gene edited mutants of DEB1, CKX2 and TB1 were developed in the rice cv. MTU1010, and these mutants are now being analysed for identification of exogenous introduced DNA free lines, and are expected to enter field trials in kharif 2024. Similarly, NRRI Cuttack has developed IPA1 edited lines of Swarna, and these mutants are now being analysed for identification of exogenous introduced DNA free lines, and are expected to enter field trials in kharif 2024.

For globally competitive agriculture deployment of genome editing technologies are essential as improved varieties with yield, nutritional quality and climate resilience with less agrochemical requirements can be developed and deployed in a cost-effective manner. The Indian Council of Agricultural Research proposes a project on “Enhancing climate resilience and ensuring food security with genome editing tools” for fast tracking the development crop varieties with improved yield, nutritional quality and climate resilience by using genome editing.