In News:

The National Institute of Plant Genome Research (NIPGR), New Delhi, has successfully used CRISPR-Cas9 gene-editing technology to develop japonica rice lines with enhanced phosphate uptake, leading to up to 40% higher yield under limited fertilizer conditions. The research is published in the Plant Biotechnology Journal.

Background: Phosphorus and Agriculture

• Phosphorus (P) is vital for plant growth, involved in photosynthesis, energy transfer, and root development.
• However, only 15–20% of phosphate fertilizers are absorbed by crops; the rest is lost due to leaching or chemical fixation in soils.
• India imports ~4.5 million tonnes of DAP (Diammonium Phosphate) annually, making it crucial to improve P-use efficiency.

The Innovation: CRISPR-Based Precision Editing

• Target Gene: OsPHO1;2, a phosphate transporter responsible for P movement from root to shoot.
• Repressor Gene Identified: OsWRKY6, a negative regulator of OsPHO1;2.
• Initial approach (complete knockout of repressor) caused negative effects due to loss of other essential functions.
• Final strategy: Only the 30 base-pair binding site of OsWRKY6 on the promoter was deleted using CRISPR-Cas9, ensuring:
  • Increased transporter expression
  • Normal functioning of other plant processes
  • Enhanced phosphate transfer and absorption

Key Outcomes:

• Yield Increase:
  • 20% with full phosphate dose
  • 40% with only 10% of recommended fertilizer
• Improved panicle number and seed count
• No compromise on seed size, starch content, or quality
• Roots acted as efficient phosphate sinks, absorbing more P from soil
• Gene-editing localized to promoter site, ensuring minimal genetic disturbance

Safety and Regulatory Assurance

• No off-target effects: Verified using leading in silico tools and genome analysis
• No foreign DNA in final seeds: Foreign genes (e.g., Cas9, Agrobacterium vector) eliminated via Mendelian segregation
• Plants with precise edits were screened and only accurate lines were cultivated further

Significance for India

• Phosphorus-deficient soils are common across India, especially in alkaline or acidic regions
• Potential application to indica rice varieties, widely grown in India
• Supports sustainable agriculture by reducing fertilizer usage and environmental runoff
• Strengthens food security and reduces import dependency on fertilizers

About Japonica Rice:

• One of the two main varieties of Oryza sativa (the other is Indica)
• Short, sticky grains; grown primarily in Japan, Korea, China, and other East Asian countries
• Model variety used: Nipponbare, due to ease of genetic manipulation
• Japonica is commonly used in research; adaptation to Indian indica cultivars is under process