The Indian Council of Agricultural Research (ICAR) has developed India’s first fully annotated Telomere-to-Telomere (T2T) reference genome of pigeonpea (Cajanus cajan), commonly known as arhar or tur, using the popular variety ‘Asha’. The genome has been approved as the global reference genome for pigeonpea, replacing earlier partial assemblies. It is expected to accelerate the breeding of climate-resilient, high-yielding and nutritionally enriched pigeonpea varieties, strengthening India’s drive for pulse self-reliance.
What Is a Telomere-to-Telomere Genome?
Every living organism carries its hereditary information in the form of DNA (deoxyribonucleic acid), organised into thread-like structures called chromosomes. The complete set of an organism’s DNA is known as its genome. In higher plants and animals, the ends of linear chromosomes are capped by specialised structures called telomeres, which protect the chromosome from damage, much like the plastic tips on the ends of a shoelace.
A reference genome is a standard digital map of the DNA sequence of a species. It serves as the baseline against which the genomes of other individuals or varieties of that species are compared, allowing scientists to pinpoint the genes responsible for particular traits.
Sequencing a genome from one telomere to the other, hence the term Telomere-to-Telomere (T2T), means decoding the chromosome in one continuous, gap-free stretch. Conventional draft genomes, by contrast, contain gaps, particularly in centromeres (the dense central region of a chromosome that helps organise it during cell division) and other highly repetitive regions that resist standard sequencing machines. A T2T assembly reads through these difficult zones as well, producing a complete and highly accurate picture of the genome.
Analogy · The Complete City Map Expand analogy
Think of a draft genome as an old street map that shows the main roads but leaves several localities blank. A T2T genome is like a complete digital map in which every lane, alley and cul-de-sac is drawn, including the busiest junctions at the centre of the city. With the full map, you can find any address and plan any route with confidence.
The ‘Asha’ Genome Assembly at a Glance
The newly completed pigeonpea genome spans 752.65 million base pairs of DNA, assembled into 92 contigs (contiguous stretches of sequence). It provides a complete representation of all 11 chromosomes of pigeonpea, including all 11 centromeres and 22 telomeres, which demonstrates chromosome-level completeness.
Beyond the raw sequence, the genome has been annotated, which means scientists have identified and mapped the functional elements within it. The analysis catalogued 36,557 genes that together produce 48,008 messenger RNA (mRNA) transcripts, the molecules that carry instructions from DNA to build proteins. Transcriptome mapping, the comparison of these sequences against actual RNA reads, recorded more than 99.9 per cent read alignment, confirming the high accuracy and completeness of the assembly.
The assembly, designated NIPB_CcT2T_4, has been deposited in the National Center for Biotechnology Information (NCBI) database, the world’s largest public repository of genetic data, under accession number GCF_000230855.1. It was released in the global database on 20 April 2026.
The work builds on the efforts of the ICAR–National Institute for Plant Biotechnology (NIPB), New Delhi, which has led the institute’s pigeonpea genomics programme since it sequenced the same variety for the first time in 2011.
| Feature | Detail |
|---|---|
| Crop | Pigeonpea (Cajanus cajan L. Millsp.) |
| Variety | ‘Asha’ (ICPL 87119) |
| Genome size | 752.65 million base pairs |
| Contigs | 92 |
| Chromosomes | 11 (all centromeres and telomeres) |
| Genes identified | 36,557 |
| mRNA transcripts | 48,008 |
| Read alignment | More than 99.9 per cent |
| Assembly name | NIPB_CcT2T_4 |
| Global database | NCBI (accession GCF_000230855.1) |
| Release date | 20 April 2026 |
Why Pigeonpea Matters for India
Pigeonpea is one of India’s most important pulse crops and a major source of dietary protein, especially for vegetarian households. Its split grain forms arhar dal or tur dal, a staple in kitchens across the country.
India is the world’s largest producer and consumer of pigeonpea, contributing more than 75 per cent of global production. The crop is grown mainly as a kharif (monsoon season) crop, largely under rainfed conditions in the semi-arid regions of central and western India, and is the second most important pulse after chickpea (gram).
The plant is prized for more than its grain. It belongs to the legume family, and through a symbiosis with soil bacteria it can fix atmospheric nitrogen, converting it into a form usable by plants. This naturally enriches the soil and reduces the need for chemical fertilisers. Its deep taproot helps it survive prolonged dry spells and improves soil structure, which is why it is frequently grown in intercropping systems with sorghum, pearl millet, cotton or groundnut, and also serves as a protective cover against soil erosion.
Despite its importance, pigeonpea productivity in India has long lagged behind demand. Yields are constrained by pests and diseases such as Fusarium wilt (a soil-borne fungal disease) and Sterility Mosaic Disease (SMD) (a viral disease spread by mites), which can destroy a large share of the crop. Drought and erratic rainfall, becoming more frequent with climate change, add further stress. The country has therefore remained dependent on imports of tur, mainly from African nations such as Mozambique and Tanzania, to bridge the gap between demand and domestic production.
The complete genome of the crop is thus not a mere academic exercise. It gives breeders the precise genetic roadmap to tackle these weaknesses head-on and cut India’s import bill.
From Draft to Complete: 15 Years of Pigeonpea Genomics
The latest breakthrough is the culmination of a journey that began more than a decade ago. In 2011, the ICAR–National Institute for Plant Biotechnology, New Delhi, published the world’s first draft genome of a pulse crop using the ‘Asha’ variety. That milestone was also notable because it was the first crop genome to be sequenced entirely in India, by a network of Indian institutions supported by ICAR.
An improved version of the draft genome followed in 2017. The newly completed Telomere-to-Telomere sequence, released 15 years after the first draft, represents the first fully assembled reference genome for the variety and fills the gaps that earlier versions could not resolve.
The variety chosen for this feat, ‘Asha’, is itself a landmark of Indian agriculture. Bred at ICRISAT (the International Crops Research Institute for the Semi-Arid Tropics), based in Hyderabad, and released in 1993, ‘Asha’ (ICPL 87119) is a medium-duration variety recommended for central and southern India. It is valued for its bold seeds, its resistance to Fusarium wilt and Sterility Mosaic Disease, and its good dhal (split grain) quality. Its name, meaning “hope”, is fitting: the same variety that carried India’s first pulse genome draft now anchors the global reference genome.
| Year | Milestone |
|---|---|
| 1993 | ‘Asha’ pigeonpea variety released for cultivation |
| 2011 | World’s first draft genome of a pulse crop, sequenced entirely in India |
| 2017 | Improved version of the pigeonpea draft genome published |
| 2026 | Complete Telomere-to-Telomere genome approved as the global reference |
What the Complete Genome Will Enable
A complete reference genome transforms the speed and precision of crop improvement. Scientists can now scan the full genetic code to locate the genes responsible for yield, stress tolerance, disease resistance and nutritional quality, and then use that knowledge in several ways.
Molecular breeding allows breeders to select plants carrying desirable genes using DNA markers rather than waiting for the trait to show up visually in the field. Genome editing tools such as CRISPR can make precise, targeted changes in the DNA to improve a specific trait while leaving the rest of the plant unchanged. Pangenome analysis, comparing the complete genomes of many varieties, reveals the full range of genetic diversity available in the crop, including valuable genes from wild relatives.
Together, these techniques promise to shorten the breeding cycle for new pigeonpea varieties from the traditional 7 to 10 years to just a few. In practical terms, this means varieties that tolerate drought and heat, resist Fusarium wilt and Sterility Mosaic Disease, and produce grains richer in protein and micronutrients could reach farmers far more quickly.
The global approval of the ‘Asha’ sequence also means that researchers worldwide will use this genome as their common reference point, aligning their data and breeding programmes. This gives India a leadership position in pigeonpea genomics, since the genetic resource is now owned and driven by Indian science.
The Push for Pulse Self-Reliance
The genome breakthrough comes at a time when the government is working to end India’s dependence on pulse imports. The Mission for Aatmanirbharta in Pulses, announced in the Union Budget 2025-26 and approved by the Union Cabinet in October 2025, is a centrally sponsored scheme with an outlay of ₹11,440 crore, running from 2025-26 to 2030-31. It focuses on three pulses, tur (pigeonpea), urad (black gram) and masoor (red lentil), which together account for the largest production gaps.
The mission aims to expand the area under pulses to 310 lakh hectares and raise production to 350 lakh tonnes by 2030-31, with an intermediate goal of achieving self-reliance in pulses by December 2027. Under its assured procurement component, agencies like NAFED and NCCF will buy tur, urad and masoor from registered farmers at the Minimum Support Price (MSP) for four years, giving growers the confidence to expand cultivation.
Within this framework, research and seed systems occupy a central place. The mission seeks to distribute certified seeds of improved varieties across large areas, and the availability of a complete pigeonpea genome directly supports this objective. A national reference genome of this quality is the raw material for producing the next generation of high-yielding, climate-adaptive pigeonpea varieties that the mission’s targets depend upon.
The timing is deliberate. The Union Agriculture Minister has repeatedly called on the scientific community to pursue non-GMO (genetically modified organism) approaches to raise pulse productivity. Genome-informed breeding and editing that works within the plant’s own gene pool offers precisely such a path, one that can boost yields without relying on foreign-modified seeds.
Key Takeaways
- The Indian Council of Agricultural Research (ICAR) has developed India’s first fully annotated Telomere-to-Telomere (T2T) reference genome of pigeonpea (Cajanus cajan) using the ‘Asha’ variety.
- The genome has been approved as the global reference genome for pigeonpea, replacing earlier partial assemblies.
- The assembly contains 752.65 million base pairs covering all 11 chromosomes, including all 11 centromeres and 22 telomeres, and has identified 36,557 genes.
- The genome assembly, designated NIPB_CcT2T_4, was deposited in the NCBI database under accession GCF_000230855.1 and released on 20 April 2026.
- In 2011, the ICAR–National Institute for Plant Biotechnology (NIPB) had published the world’s first draft genome of a pulse crop, the first crop genome sequenced entirely in India.
- Pigeonpea is India’s second most important pulse after chickpea, with India contributing more than 75 per cent of global production.
