Chinese researchers, primarily from the Chinese Academy of Sciences, have developed the first-ever pangenome for Asian rice by analyzing 144 varieties of wild and cultivated rice. This breakthrough provides a comprehensive map of rice genetic diversity, helping improve crop resilience and productivity.
What is a Pangenome?
- A pangenome is a collection of genome sequences from many individuals of the same species.
- Unlike traditional reference genomes (which only map characteristic/common genes), a pangenome includes both Core genes shared by all varieties and Unique genes found only in specific wild or cultivated varieties
- Enables a more complete view of genetic variation within a species.
- Offers a more comprehensive view than traditional reference genomes (which only capture a single or limited sample)
Key Findings of Rice Pangenome Study
- Total Varieties Analyzed: 144 (wild and cultivated types from Asia)
- Sequencing Technology Used: PacBio High-Fidelity (HiFi) Single-Molecule Real-Time (SMRT) sequencing
- Novel DNA Sequences Identified: 3.87 billion base pairs not found in the existing Oryza sativa ssp. japonica reference genome
- Total Genes Identified: 69,531
- Core Genes: 28,907
- Wild-Rice-Specific Genes: 13,728
- ~20% of genes are wild rice-specific
- Implications:
- Genes may hold keys to climate resilience, phenotypic plasticity, and disease resistance
- Can help develop next-gen rice varieties with traits from wild rice
Evolutionary Insights
- Study confirms that all Asian cultivated rice (Oryza sativa L.) evolved from a wild progenitor species Oryza rufipogon.
- Subgroup Or-IIIa is identified as the direct ancestor of japonica rice.
- Indica rice likely emerged from cross-breeding between ancient japonica and Or-I population of O. rufipogon in southern Asia.
Benefits of Rice Pangenome
- Enhances understanding of:
- Environmental adaptation
- Phenotypic plasticity (how a plant adapts to environment)
- Regeneration potential in rice varieties
- Bridges wild and cultivated rice genetics
- Aids in developing climate-resilient, disease-tolerant and high-yielding rice varieties
Global & Indian Context
Global Importance of Rice:
- Staple food for nearly two-thirds of the world population
Indian Highlights:
- 2024-25 Production: 220 million tonnes
- Area Cultivated: 51,000 hectares
- Average Yield: 4.2 tonnes/hectare
- Climate Concern: 2024 was the hottest year, with minimum temperature 0.9°C above average
Indian Research Update:
- In May 2025, ICAR developed two genome-edited rice varieties:
- Samba Mahsuri
- MTU 1010
- Claimed benefits: Higher yield & drought resistance
- Current Status: Not yet released for commercial farming
About HiFi (High-Fidelity) Sequencing Technology
- A long-read sequencing method offering:
- High accuracy
- Long DNA read lengths
- Suited for complex genome analysis like pangenomes
Applications of Pangenome
| Sector | Benefits |
| Agriculture | Develop resilient crops; improve yields; fight climate change |
| Medicine | Identify population-specific disease markers (e.g., Human Pangenome Project) |
Significance for Agriculture
Like the Human Genome Project, this study bridges gaps in genetic data and opens up opportunities for:
- Creating superior, resilient rice varieties
- Enhancing yield, drought tolerance, and adaptability to climate change
- Combating rising temperatures and arsenic uptake