News: Scientists have created the first-ever ‘pangenome’ for rice by combining essential genetic segments from 144 wild and cultivated rice varieties across Asia to form a comprehensive reference genome. Pangenome.
About Pangenome
- A pangenome is a comprehensive collection of genome sequences from multiple individuals of the same species.
- It aims to capture the full range of genetic variation across a population, offering a broader reference for genomic comparisons.
- Scientists use pangenomes as reference genomes to compare with new individual genomes. This helps in identifying genetic variants that may affect traits, health, or disease susceptibility.
About Pangenome of Asian Rice
- A pangenome includes both core genes shared across all rice varieties and unique genes from individual strains. It provides a comprehensive genetic map of Asian rice, aiding in crop improvement.
- Significance for India: India, a key rice producer, recorded 220 million tonnes of production in 2024–25 across 51,000 hectares with an average yield of 4.2 tonnes/hectare. The new pangenome database supports the development of climate-resilient and disease-tolerant rice varieties.
Key Scientific Findings
- Scientists have developed the first-ever rice pangenome by combining genomic sequences from 144 wild and cultivated rice varieties across Asia.
- The study reveals 3.87 billion base pairs of novel genetic sequences that were missing in the previously used single reference genome.
- A total of 69,531 genes were identified across the pangenome:
- 28,907 core genes common to all varieties.
- 13,728 genes specific to wild rice.
- Approximately 20% of the total genes were unique to wild rice, offering critical insights into environmental adaptation and potential for breeding improvements.
- The research supports the hypothesis that all Asian cultivated rice originated from a wild rice variety known as Or-IIIa, an ancestor of japonica rice.
- Population genetics analysis confirms that japonica rice was the first to be domesticated from O. rufipogon group IIIa in China. Later, indica rice evolved through hybridization with local wild rice (Or-I) populations as japonica spread across Asia.
- The use of PacBio HiFi sequencing and advanced computational tools allowed for a deep analysis of gene flow and evolutionary pathways between domesticated and wild rice varieties.
- The study significantly enhances understanding of rice domestication, phenotypic diversity, and resilience, providing a foundation for breeding superior, climate-resilient, and high-yield rice cultivars.
