World's 1st Rice Variety Using 21st Century "Genome Editing" Produced In India

1. The Indian Council of Agricultural Research (ICAR) has successfully developed the world’s first genome-edited (GE) rice varieties using CRISPR-Cas technology.
2. These varieties have been developed without introducing any foreign DNA, making them distinct from genetically modified (GM) crops.
3. This achievement marks a major step in the advancement of precision agriculture in India.
4. The development of such varieties adds to India's growing agricultural export, with Rs 48,000 crore worth of Basmati rice being exported annually.
5. Institutions Involved
   1. Indian Institute of Rice Research (IIRR) – Hyderabad
   2. Indian Agricultural Research Institute (IARI) – New Delhi
6. These institutions are affiliated with Indian Council of Agricultural Research and jointly contributed to the research and development of the genome-edited rice varieties.

Research Methodology

1. Selection of Varieties: Scientists selected 2 highly cultivated varieties for improvement:
   1. Samba Mahsuri (BPT5204): Known for fine grain quality but vulnerable to climate stress.
   2. MTU1010 (Cottondora Sannalu): High yielding but sensitive to drought and soil salinity.
2. Genome Editing: ICAR enhanced these varieties to make them more resilient to stress, improve yield, and provide better climate adaptability.

Technology Used : Genome Editing Technology

1. CRISPR-Cas9 System: This technique leads to desirable traits like increased yield, climate resilience, and improved disease resistance without the introduction of foreign DNA.

What is CRISPR-Cas9? A gene-editing tool that lets scientists change DNA with precision. Uses a guide RNA and Cas9 protein to target and cut specific parts of the DNA. Key Components Guide RNA (gRNA): A small RNA molecule that directs the Cas9 protein to the target DNA sequence. Acts like a "GPS" for the Cas9 protein. Cas9 Protein: An enzyme that cuts the DNA at the location specified by the gRNA. Works like "molecular scissors." How CRISPR-Cas9 Works: The gRNA is designed to match the DNA sequence to be edited. The Cas9 protein attaches to the gRNA. The gRNA-Cas9 complex finds the matching DNA sequence. Cas9 cuts the DNA at the target location. The cell’s natural repair process fixes the DNA cut, leading to possible changes in the sequence (adding/deleting base pairs). Applications: Disease Treatment: Can correct genetic mutations causing diseases. Basic Research: Helps understand gene functions and their roles in processes. Agriculture: Used to improve crop traits like disease resistance. Developing Therapies: Helps in creating new treatments and drugs for diseases.

2. Methods Applied:  ICAR used SDN-1 for both rice varieties.
3. Cas Enzymes Used:
   • CRISPR-Cas12 for Samba Mahsuri (Kamala)
   • CRISPR-Cas9 for MTU-1010 (Pusa DST Rice 1)

What is Site-Directed Nucleases (SDN)

Type	Description	Regulatory Status in India
SDN-1	Cuts DNA at a specific site, natural repair occurs without a DNA template or foreign gene	Allowed
SDN-2	Cut + small template from same species guides precise edits	Allowed
SDN-3	Insertion of foreign genes from other species	Not allowed (regulated as GMO)

DETAILS OF THE TWO GE RICE VARIETIES

2 new varieties developed through genome-editing technology:

1.  Kamala (IET-32072)
   1. Parent Variety: Samba Mahsuri (BPT-5204) – known for fine grain quality.
   2. Gene Edited: Gn1a (cytokinin oxidase 2) → controls grain per panicle.
   3. Editing Objective: Downregulation → increased grains/panicle → improved yield.
   4. Technology Used: CRISPR-Cas12
   5. Maturity: 130 days (15–20 days earlier than parent)
   6. Yield:
      1. Average: 5.37 tonnes/ha
      2. Potential: 9 tonnes/ha
      3. (Parent: Avg. 4.5 t/ha; Potential: 6.5 t/ha)
   7. Cultivation Zone: ~5 million ha in TN, AP, Telangana, Odisha, WB, Bihar, Chhattisgarh, Jharkhand, eastern UP.
2. Pusa DST Rice 1 (IET-32043)
   1. Parent Variety: MTU-1010 (Cottondora Sannalu) – popular Rabi crop.
   2. Gene Edited: DST (Drought and Salt Tolerance) gene.
   3. Objective: Introduce abiotic stress tolerance (drought/salinity).
   4. Technology Used: CRISPR-Cas9
   5. Maturity: 125–130 days
   6. Cultivation Zone: ~4 million ha in southern, central, and eastern India.

Yield under Stress Conditions:

Condition	GE Yield (t/ha)	Parent Yield (t/ha)
Inland salinity	3.508	3.199
Alkaline soils	3.731	3.254
Coastal salinity	2.493	1.912

Features of Genome-Edited Rice Varieties

1. Yield Increase: The new rice varieties provide a 25% higher yield compared to traditional rice varieties.
2. Water Efficiency: These varieties require less water, saving a significant amount in irrigation.
3. Climate Resilience: Designed to be more climate-resilient and adaptable to varying environmental conditions.

Significance and Benefits

1. Environmental Benefits: These varieties are designed to reduce greenhouse gas emissions (by 20%) and save up to 7,500 million cubic meters of water for irrigation.
2. This can be used for other crops, improving the overall water-use efficiency in agriculture.
3. Impact on Climate Change: The new varieties can address challenges posed by climate change, such as rising temperatures, irregular rainfall, and water scarcity.
4. Global Historical Milestone: India became the first nation to produce genome-edited rice varieties, marking a significant step in global agricultural innovation.

Not a GM Crop

1. Non-GM: These rice varieties are not genetically modified (GM). No foreign DNA has been introduced into the plants.
2. The genome editing done is within the existing genetic material of the rice, making them safe and free from the controversies surrounding GM crops.

Key Differences Between Genome-Edited (GE) and Genetically Modified (GM) Crops:

Aspect	Genome-Edited (GE) Crops	Genetically Modified (GM) Crops
Definition	Editing of native genes within the plant’s own genome	Insertion of genes from unrelated species into the plant genome
Use of Foreign DNA	No foreign DNA is used	Foreign DNA from other organisms is introduced
Example	Kamala and Pusa DST Rice 1 (edited versions of Samba Mahsuri and MTU-1010)	Bt cotton (contains genes from Bacillus thuringiensis)
Technology Used	CRISPR-Cas with SDN-1 or SDN-2	Recombinant DNA technology

 

Regulation of Gene Editing in Agriculture in India:

Regulatory Aspect	Gene Editing in India
GMO Regulation	GMOs are regulated under the ‘Rules for the Manufacture, Use, Import, Export and Storage of Hazardous Microorganisms/ Genetically Engineered Organisms or Cells, 1989 under the Environment Protection Act (EPA), 1986. Regulated by GEAC (Genetic Engineering Appraisal Committee) GEAC (Genetic Engineering Appraisal Committee) – Approves large-scale use and environmental release Statutory body under the Environment (Protection) Act, 1986. Works under Ministry of Environment, Forest and Climate Change. Can take legal action if rules are violated.
Mention of Gene Editing	No explicit mention of gene editing in the existing regulations
Amendment	An amendment was introduced to encourage gene editing in agriculture
Techniques Using Native Genome (SDN-1, SDN-2)	Allowed under the EPA, 1986 regulations as they do not involve foreign DNA
Techniques Using Foreign Genome (SDN-3, SDN-4, SDN-6)	Not allowed in India; these fall under GMO regulation as they introduce foreign DNA
Gene Editing Exemption	SDN-1 and SDN-2 are exempt from stringent GMO regulation due to their use of native genes

Field Trials and Approval

1. Both the GE rice varieties were tested under multi-location field trials.
2. These trials were conducted in 2023 and 2024.
3. The trials were part of the All India Coordinated Research Project (AICRP) on Rice.
4. The Department of Biotechnology’s Review Committee on Genetic Manipulation (RCGM) approved the trials and confirmed that the varieties are free from exogenous DNA.
5. This allowed the varieties to be treated as non-GM crops.

Launch and Government Support

1. In the Union Budget 2023–24, the Government of India allocated ₹500 crore to promote genome-editing research in agriculture.
2. ICAR is using this funding to expand gene-editing efforts to other crops.
3. These include pulses, oilseeds, livestock breeds, fish species, and beneficial microbes.
4. GE crops under SDN-1 & SDN-2:
   1. Declared equivalent to conventionally bred lines
   2. Approved for multi-location trials and commercial release
   3. Not regulated as GMOs

Intellectual Property Rights (IPR) Issues

1. The CRISPR-Cas9 gene-editing system is patented by the Broad Institute of MIT and Harvard.
2. Its use in India is under license.
3. ICAR has acknowledged that intellectual property rights (IPR) issues exist regarding this technology.
4. However, the organization has stated that these concerns are being addressed and will be resolved in due course.

GM Crops in India :

1.  Approved GM Crop
   1. Bt Cotton (since 2002)
      1. Why used? Resists cotton bollworm.
      2. How? Contains genes from Bacillus thuringiensis (Bt), which produce Cryoproteins toxic to insects.
2.  Pending/Restricted GM Crops
   1. Bt Brinjal
      1. Approved in 2009 by GEAC, but put on hold (moratorium).
      2. Contains cry1Ac gene from Bt for insect resistance.
      3. Field trials for two new types (Janak & BSS-793) were allowed in 8 states.
   2. GM Mustard (DMH-11)
      1. Developed by Delhi University’s Centre for Genetic Manipulation of Crop Plants.
      2. Not yet released for commercial use.
      3. Made by crossing two mustard types: Varuna & Early Heera-2 (normally self-pollinating).
      4. Genes Used:
         1. Barnase – Makes plant male-sterile (stops self-pollination).
         2. Barstar – Reverses barnase effect in hybrid, allowing fertility.
         3. Bar – Gives resistance to herbicide "Basta" (for selection).
      5. Goal: Create a high-yield hybrid mustard.

Concerns with GM Crops

1. Ecological Risks
   1. Genetic contamination of wild species.
   2. Pest and weed resistance (e.g., pink bollworm, whitefly).
   3. Harm to non-target species like butterflies.
2. Biodiversity Threat
   1. Soil damage from GM proteins.
   2. Harm to helpful microbes and insects.
3. Economic & Ethical Issues
   1. Yields not always better (Bt cotton stagnation).
   2. Corporate control of seeds = market monopoly.
   3. Ethical worries about long-term effects.
   4. Risk of allergens in food.

Recommendations (Parliamentary Committee)

1. Better Regulation – More transparency in GEAC, include MPs in district panels.
2. Scientific Review – Do real-world trials, measure true yield, pesticide use, and environmental impact.
3. Labeling – Make GM food labeling mandatory for informed consumer choice.
4. Animal Studies – Test effects on livestock and fish.
5. National GM Policy – Clear policy for GM crop research, farming, and trade.

 

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