Asian Rice Pangenome

PWOnlyIAS

May 10, 2025

Asian Rice Pangenome

Scientists have created the first-ever Asian rice pangenome, encompassing genetic data from 144 wild and cultivated rice varieties.

What is a Pangenome?

  • A pangenome is a comprehensive genomic resource that includes both core genes shared by all individuals and unique genes found in some individuals of a species.
  • It offers a more complete picture of genetic variation than a traditional reference genome.

Significance for Rice Genetics and Food Security

  • Global Importance: Rice (Oryza sativa L.) is a staple food for two-thirds of the global population and a critical crop in Asia.
  • Genetic Benefits: Understanding genetic diversity helps improve disease tolerance, climate resilience, and nutritional quality of rice.
  • Domestication Link: The study strengthens knowledge of rice domestication, linking modern rice to wild progenitor O. rufipogon, particularly the Or-IIIa group, ancestor of japonica rice.
  • Stress Adaptation: The pangenome offers genetic resources to enhance rice’s adaptation to environmental stress and regenerative potential.

Differences between a Pangenome and a Reference Genome

Feature Reference Genome Pangenome
Definition Genome of a single representative variety Combined genomic data from multiple varieties
Gene Coverage Includes only the genes present in one variety Includes both core (shared) and unique genes from many varieties
Core Genes Identified Not specifically categorized 28,907 core genes shared among all studied varieties
Unique/Wild-Specific Genes Typically not included Includes 13,728 wild-rice-specific genes
Genetic Material Coverage Limited to one genome Contains 3.87 billion base pairs of novel sequences not in the reference genome
Genetic Diversity Representation Low High as it captures broader genetic variation
Utility Basic genetic reference Enables identification of novel traits and improved trait mapping
Use in Breeding Programs Limited applicability High potential for developing stress-tolerant and high-yield varieties

Applications in Crop Resilience and Breeding

  • The pangenome enables scientists to:
    • Develop new rice cultivars with better resistance to drought and diseases
    • Transfer beneficial traits from wild rice to cultivated rice
    • Address climate change impacts, such as yield loss and increased arsenic uptake
  • Using ‘PacBio high-fidelity’(HiFi) sequencing technology and computational methods, the analysis revealed 3.87 billion base pairs of novel genetic sequences.
    • These Genome data can guide precision breeding for yield enhancement, stress tolerance, and climate adaptation.

Status of India’s Rice Production and Research

  • India produced a record 220 million tonnes of rice in 2024–25 with an average yield of 4.2 tonnes/ha.
  • In 2024, the Indian Council of Agricultural Research (ICAR) announced genome-edited varieties like Samba Mahsuri and MTU 1010 with improved drought resistance and higher yields.
  • India’s rising temperatures (0.7°C since 1901; 2024 was the hottest year on record) make such research critical for national food security.

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Quick Revise Now !
UDAAN PRELIMS WALLAH
Comprehensive coverage with a concise format
Integration of PYQ within the booklet
Designed as per recent trends of Prelims questions
हिंदी में भी उपलब्ध

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