Pangenome of Asian Rice: Development Process and Significance

Scientists have successfully created the first pangenome of Asian rice (Oryza sativa), a monumental step to enhance rice breeding. Discover how this comprehensive genetic map will accelerate the development of climate-resilient and higher-yielding rice varieties.

Table of Contents

Context: Scientists have created a ‘pangenome’ by stitching together key parts of genomes from 144 varieties of wild and cultivated varieties of rice from Asia.

What is a Pangenome?

Pangenome is a complete collection of all the genes found in different types of a species.
It includes:
- Core genes – shared by all types (common genes)
- Unique genes – found only in some types, like wild or special varieties.
This gives a full picture of genetic diversity, unlike a single reference genome, which shows only one version.

“Simplified”

A single reference genome is like reading one book to understand a whole library — it gives you an idea, but misses many details.
In contrast, a pangenome combines genetic data from many different varieties (both wild and cultivated). So instead of seeing just one version of the species, you see all the differences and similarities between them.

Development Process

Scientists used 144 varieties of wild and cultivated Asian rice (Oryza sativa L.).
Sequencing was done using PacBio HiFi (High-Fidelity) technology.
Computational methods were used for deep genetic analysis.
The focus was on gene flow within cultivars and between cultivated and wild rice.

Significance

Enables the development of resilient, high-yielding rice varieties.
Can incorporate traits from wild rice, improving:
- Drought resistance
- Disease tolerance
- Climate change adaptability.

High-Fidelity (HiFi) Sequencing Technology

It’s a single-molecule, real-time sequencing (SMRT) technology.
It’s known for its exceptionally high accuracy in reading individual DNA molecules across long stretches.
It falls under the category of Long-read sequencing methods used in genome sequencing.
- Long-read sequencing, in general, allows for the sequencing of significantly longer DNA fragments compared to conventional short-read sequencing techniques.

Key Facts

Rice is the staple food for two-thirds of the world’s population.
India’s Rice Production (2024–25): 220 million tonnes.
Climate Change Impact: Threatens yields, increases arsenic uptake in rice varieties.
New Genome-Edited Varieties (ICAR): Samba Mahsuri and MTU 1010.