ICAR marks a first, develops two genome-edited varieties of rice
The Indian Council of Agricultural Research (ICAR) said it has developed the world's first genome edited (GE) rice varieties with superior yields, drought and salinity tolerance, and high nitrogen-use efficiency traits.
Two of its affiliate institutions — the Hyderabad -based Indian Institute of Rice Research (IIRR) and the Indian Agricultural Research Institute (IARI) at New Delhi — have bred improved GE mutants of the popular Samba Mahsuri (BPT-5204) and Cottondora Sannalu (MTU-1010) varieties using CRISPR-Cas SDN-1 (Site-Directed Nucleases-1) technologies.
Union Minister of Agriculture and Farmers' Welfare Shivraj Singh Chouhan released the two rice varieties at the ICAR's NASC Complex on Sunday.
GE is different from genetic modification or GM. The latter involves introduction of genes from unrelated species into host plants. These could, for example, be genes from Bacillus thuringiensis, a soil bacterium, that code for the production of proteins toxic to various insect pests in cotton.
GE, on the other hand, 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.
CRISPR-Cas uses 'Cas' enzymes, or proteins that act like molecular 'scissors', to cut and modify the DNA sequence of a native gene at its targeted location. Such editing is intended to bring forth desirable alterations in that gene's expression and function.
In this case, scientists at IIRR have used the CRISPR-Cas12 protein for editing the 'cytokinin oxidase 2' gene (also called Gn1a) in Samba Mahsuri rice, in order to the increase the number of grains produced from each panicle (plant earhead) of this variety.
The Gn1a gene basically codes for an enzyme that regulates the number of grains per panicle, thereby indirectly influencing yields. Through 'editing', the scientists are able to reduce the expression of that gene, leading to an increase in the number of grains per plant.
The Samba Mahsuri rice variety is extensively cultivated in about five million hectares (mh) across Tamil Nadu, Andhra Pradesh, Telangana, Karnataka, Odisha, Chhattisgarh, West Bengal, Bihar, Jharkhand and eastern Uttar Pradesh.
The new GE line – called IET-32072 or 'Kamala' – is claimed to have recorded an average paddy (rice with husk) yield of 5.37 tonnes per hectare with a potential of 9 tonnes. This is higher than the corresponding average and potential yields of 4.5 tonnes and 6.5 tonnes/hectare from its parent Samba Mahsuri (BPT-5204) variety.
Further, 'Kamala' matures in about 130 days (from seed to grain), 15-20 days earlier than Samba Mahsuri, but has the same grain attributes and cooking quality 'exactly like the original variety', according to an ICAR statement.
The CRISPR-Cas9 protein has been used similarly to edit the 'DST (drought and salt tolerance)' gene in the MTU-1010 or Cottondora Sannalu rice variety, which is grown in 4 mh across southern, central and eastern India. The variety is popular for its high yields (potential of 7 tonnes/hectare), early duration (125-130 days), and producing long slender grains.
The new GE mutant of MTU-1010 will enable this variety to also be cultivated in areas prone to drought and salinity stress.
The GE SDN-1 mutant line – called IET-32043 or Pusa DST Rice 1 – is claimed to have recorded an average paddy yield of 3.508 tonnes/hectare under inland salinity stress conditions, compared to 3.199 tonnes of the parent (MTU-1010) variety).
It has also given an average of 3.731 tonnes/hectare under alkaline and 2.493 tonnes/hectare under coastal stress conditions, as against the corresponding yields of 3.254 tonnes and 1.912 tonnes per hectare respectively.
India has exempted GE crops from biosafety regulations under the Environment (Protection) Act of 1986. These regulations govern both field trials and release for commercial cultivation in the case of GM crops that are treated as 'hazardous substances' under the Act.
The GE mutants created through SDN-1 and SDN-2 techniques are free of foreign genes or exogenous DNA. Their 'release' into the environment is, hence, seen to not pose risks and require multi-year trials and approvals, if at all, from the Genetic Engineering Appraisal Committee under the Ministry of Environment, Forest and Climate Change.
Both the improved GE varieties were tested in multi-location field trials under the All India Coordinated Research Project on Rice during 2023 and 2024. This followed the approval from the Department of Biotechnology's Review Committee on Genetic Manipulation to consider these as 'free of exogenous introduced DNA' and 'equivalent to conventional mutant/breeding lines'.
The ICAR statement said that the development of the two GE rice varieties has paved the way for using this technology for higher yields, climate resilience, and improved quality traits in oilseeds, pulses and other crops too. The 2023-24 Union Budget had allocated Rs 500 crore for GE breeding and research in agriculture.
The statement conceded there are still issues over intellectual property rights on the CRISPR-Cas9 technology, which is patented by the Broad Institute of MIT and Harvard. Its use is licensed. The IPR concerns 'are being looked after and will be resolved in coming times,' ICAR said.
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