Pangenome

About Pangenome

• A pangenome includes not only the core genes shared by all varieties but also the unique genes found in individual strains, offering a comprehensive map of genetic diversity in Asian rice.
• This project is comparable to the Human Genome Project (2003) in its goal to map genome-wide variations, but it is focused on rice, which is a staple food for nearly two-thirds of the world population.
• India, a major rice producer, recorded a record production of 220 million tonnes in 2024-25 over 51,000 hectares, with an average yield of 4.2 tonnes/hectare.
• The new pangenome database enables the development of advanced rice cultivars with enhanced traits, such as disease tolerance and resilience to climate shocks.

Key Findings

• Researchers used high-fidelity sequencing (PacBio HiFi) and advanced computational tools to assemble 87 billion base pairs of novel genetic sequences, which were absent from the earlier reference genome of Oryza sativa ssp. japonica.
• A total of 69,531 genes were identified, out of which:
  • 28,907 are core genes common to all varieties,
  • 13,728 are specific to wild rice, and
  • About 20% of all genes were unique to wild rice species, offering potential for future improvements in rice breeding.
• Indian Council of Agricultural Research (ICAR) recently developed two genome-edited rice varieties – Samba Mahsuri and MTU 1010 – that show promise for higher yield and drought resistance, though they are not yet released for cultivation.

Threats

• Climate change is a significant threat to rice production in India. The country has seen an average temperature rise of 0.7°C since 1901, and 2024 was the hottest year recorded, with minimum temperatures 0.9°C above average.
• Rising temperatures also increase arsenic uptake in rice, posing risks to both health and crop yield stability