ICAR develops India’s first fully annotated T2T genome of pigeonpea variety Asha
The Indian Council of Agricultural Research (ICAR) developed a fully annotated telomere-to-telomere (T2T) genome assembly of the pigeonpea (arhar/tur) variety 'Asha'
This is described as India's first fully annotated T2T genome resource for pigeonpea, one of the country's key pulse crops
The genome resource is expected to speed up gene discovery, enable precision breeding, and support productivity gains in pigeonpea cultivation
It builds on earlier draft-level pigeonpea genome sequencing efforts undertaken over the past decade and a half
Telomere-to-Telomere (T2T) Genome Assembly
A T2T genome assembly is a complete, gap-free sequencing of a chromosome from one telomere (protective chromosome-end cap) through the centromere to the other telomere, producing a single, continuous contig per chromosome rather than a fragmented "draft" genome. It relies on long-read sequencing technologies (e.g., PacBio HiFi, Oxford Nanopore) combined with chromatin-conformation methods (Hi-C) to resolve repeat-rich regions that older short-read technologies could not assemble.
Key Details
- Traditional ("draft") genome assemblies leave unresolved gaps at centromeres, telomeres, and repetitive DNA stretches
- T2T assemblies became feasible at scale after long-read sequencing matured; the first T2T assembly of the human genome was completed and published in 2022 by the Telomere-to-Telomere Consortium
- A T2T genome provides a far more reliable reference for locating genes, structural variants, and regulatory elements than earlier draft assemblies
- Fully "annotated" adds a further layer: predicted protein-coding genes are functionally characterised (assigned probable biological roles), not just structurally identified
Earlier pigeonpea genome efforts (from international consortium-led draft sequencing in the early 2010s to improved drafts with tens of thousands of predicted genes) left gaps in complex genomic regions. A T2T assembly for 'Asha' is a qualitative upgrade — a complete, gap-free reference — that gives breeders and gene-discovery researchers a far more precise genomic map.
Pigeonpea (Cajanus cajan) in India's Pulses Economy
Pigeonpea — known as arhar, tur, or red gram — is India's second most important pulse crop after chickpea and the world's most widely grown; India is the largest producer of pigeonpea globally, accounting for the large majority of world production.
Key Details
- Contributes a significant share of India's total domestic pulse production
- Major producing states include Maharashtra (largest producer), Karnataka, Madhya Pradesh, Uttar Pradesh, Gujarat, and Jharkhand
- The Union Budget 2025-26 announced the "Mission for Atmanirbharta in Pulses," a six-year initiative to boost self-reliance in key pulses including tur (pigeonpea), urad, and masoor
- Pigeonpea is largely a rainfed kharif crop with a long duration (5-11 months depending on variety), making breeding for shorter duration and disease resistance a priority
A precision genomic resource for a widely cultivated variety like 'Asha' directly supports the Mission for Atmanirbharta in Pulses by enabling faster identification of genes for yield, disease resistance (e.g., fusarium wilt, sterility mosaic disease), and stress tolerance.
Genomics-Assisted and Precision Breeding
Precision breeding uses genomic information — marker-assisted selection, genomic selection, and increasingly genome editing — to select or introduce desirable traits faster and more accurately than conventional breeding, which relies on phenotypic selection across multiple generations.
Key Details
- A complete annotated reference genome allows researchers to pinpoint genes controlling traits like disease resistance, drought/heat/salinity tolerance, and seed weight, then design markers to track those genes in breeding populations
- This is distinct from, but complementary to, genome-editing approaches (e.g., CRISPR-Cas9 under the SDN-1/SDN-2 framework exempted from GEAC biosafety review in India since 2022)
- New pigeonpea varieties bred using such resources would be eligible for registration and protection under the Protection of Plant Varieties and Farmers' Rights (PPV&FR) Act, 2001, which grants breeder and farmer rights subject to Distinctiveness, Uniformity, and Stability (DUS) criteria
The T2T genome of 'Asha' is explicitly positioned as a tool to "speed gene discovery" and enable "precision breeding," linking this basic-science genomic milestone to applied plant-breeding outcomes for one of India's key pulse crops.
- India accounts for a large majority (roughly three-fourths or more) of global pigeonpea production
- Pigeonpea is India's second-most important pulse crop after chickpea
- Top producing states: Maharashtra, Karnataka, Madhya Pradesh, Uttar Pradesh, Gujarat, Jharkhand (together account for over 80% of national tur output)
- 'Mission for Atmanirbharta in Pulses': a six-year initiative announced in Union Budget 2025-26 covering tur, urad, and masoor
- The first human T2T genome (reference point for the technology) was completed in 2022
- Plant variety protection in India for newly bred pigeonpea varieties falls under the PPV&FR Act, 2001