Scientists create first ‘pangenome’ of Asian rice

In a major scientific breakthrough, researchers — primarily from the Chinese Academy of Sciences — have assembled the first rice pangenome, a comprehensive reference genome created by stitching together key genetic sequences from 144 varieties of both wild and cultivated rice found across Asia. This landmark achievement, akin to the Human Genome Project, represents a significant leap in our understanding of rice genetics, and is poised to revolutionize crop breeding in the face of climate change.

What Is a Pangenome?

• A pangenome incorporates the entire spectrum of genetic diversity within a species.
• Unlike traditional reference genomes (which are usually based on a single individual or variety), it reflects multiple genomes, capturing genes unique to different cultivars or wild varieties.
• In this case, scientists used ‘PacBio HiFi’ sequencing technology, known for its high accuracy and long reads, to identify 3.87 billion base pairs of novel genetic sequences missing from the existing reference genome (Oryza sativa ssp. japonica).

Key Scientific Findings

• Asian cultivated rice (Oryza sativa L.) was domesticated from O. rufipogon, a wild rice species.
• The study traced the domestication and gene flow pathways, reinforcing that all Asian cultivated rice evolved from the Or-IIIa variant, considered the ancestor of the japonica subspecies.
• Analysis revealed complex gene flows between wild and domesticated varieties, helping map evolutionary pathways and adaptation mechanisms.

Why It Matters

• Rice feeds nearly two-thirds of the world population and is India’s primary crop during the monsoon (June–September).
• In 2024–25, India recorded 220 million tonnes of rice production from 51,000 hectares, averaging 4.2 tonnes/ha.
• Climate change is increasingly affecting rice yields and quality:
  • India’s average temperature has risen by 0.7°C since 1901.
  • 2024 was the hottest year on record, with average minimum temperature 0.9°C above normal.
  • Arsenic uptake in rice has been linked to rising temperatures, posing health risks and economic loss.

(Source: TH)