Researchers have made a groundbreaking advancement in rice genetics by creating the first comprehensive pangenome of Asian rice. This detailed genetic map, encompassing 144 wild and cultivated varieties, reveals novel genes previously unknown and offers new opportunities to breed rice varieties that are stronger, more resilient to climate change, and better equipped to resist diseases
In a landmark scientific achievement, researchers—primarily from the Chinese Academy of Sciences—have successfully constructed the first comprehensive pangenome of Asian cultivated rice (Oryza sativa L.). By sequencing the genomes of 144 diverse rice varieties, both wild and cultivated, this study offers an unprecedented genetic map that could transform rice breeding. The findings pave the way for developing rice strains that are climate-resilient, high-yielding, and disease-tolerant, a critical advance amid growing concerns over global food security and climate change.
This breakthrough comes at a crucial moment as rising global temperatures threaten crop yields worldwide. India, one of the largest rice producers, recorded its hottest year on record in 2024, underscoring the urgent need for innovations that strengthen rice cultivation.
Unlike traditional reference genomes that represent only a single version of a species, a pangenome captures the full genetic diversity of a species by including both core genes shared across all varieties and accessory genes unique to specific strains. Using advanced PacBio HiFi sequencing technology, the researchers identified 69,531 genes in total. Of these, 28,907 are core genes found in all rice varieties, while 13,728 are unique to wild rice. Notably, the study uncovered 3.87 billion base pairs of genetic material absent from previous reference genomes, with about 20 per cent of the identified genes exclusive to wild rice.
The study also supports the hypothesis that all Asian cultivated rice descends from the Or-IIIa wild rice group. This vast genetic diversity provides crucial resources for enhancing disease resistance, climate resilience, and crop yield. By bridging the genetic gap between wild and cultivated rice, the pangenome gives breeders access to valuable traits that could accelerate the development of improved rice varieties.
Rice is a staple food for nearly two-thirds of the global population, and India produced a record 220 million tonnes of rice in 2024–25. However, the country faces major challenges such as rising temperatures and arsenic contamination in rice crops. While ICAR has recently developed two genome-edited rice varieties—Samba Mahsuri and MTU 1010—these are not yet available for public cultivation. The new pangenome provides an invaluable tool to help address these challenges and ensure sustainable rice production in the future.
