The Indian Council of Agricultural Research (ICAR) has developed India's first fully annotated telomere-to-telomere (T2T) reference genome of pigeonpea (Cajanus cajan L. Millsp.) variety 'Asha', the council announced on Tuesday. According to ICAR, the complete T2T genome sequence spans 752.65 million base pairs assembled into 92 contigs, providing a complete representation of all 11 chromosomes of pigeonpea. The genome assembly, designated NIPB_CcT2T_4, has been deposited in the global database NCBI.
A landmark for India's pulse economy
Pigeonpea, popularly known as 'Arhar' or 'Tur', is one of India's most important pulse crops and a major source of dietary protein, according to ICAR, playing a vital role in the country's food and nutritional security. The new T2T assembly marks the second major genome milestone for the crop: in 2011, ICAR–National Institute for Plant Biotechnology, New Delhi published the world's first draft genome of pigeonpea variety 'Asha' — the first crop genome to be sequenced entirely in India — followed by an improved draft genome in 2017, ICAR reported.
Genome assembly by the numbers
ICAR said the genome assembly includes all 11 chromosomes, including their centromeres and telomeres, demonstrating chromosome-level completeness. A comprehensive genome annotation identified 36,557 genes, producing 48,008 mRNAs (coding sequences). Transcriptome (RNA sequence) mapping recorded more than 99.9 per cent read alignment, confirming the high accuracy and completeness of the genome.
| Metric | Value |
|---|---|
| Genome assembly designation | NIPB_CcT2T_4 |
| Total genome size | 752.65 million base pairs |
| Contigs | 92 |
| Chromosomes | 11 (all, with centromeres and telomeres) |
| Genes annotated | 36,557 |
| mRNAs (coding sequences) | 48,008 |
| Transcriptome read alignment | >99.9% |
Breeding impact and policy push
The fully annotated T2T reference genome will serve as a valuable national genomic resource for advanced gene and pangenome analyses, discovery of genes associated with important agronomic and nutritional traits, and the application of molecular breeding and genome-editing technologies, ICAR said. Specifically, ICAR listed the genome's potential uses as:
- Advanced gene and pangenome analyses
- Discovery of genes associated with important agronomic and nutritional traits
- Application of molecular breeding and genome-editing technologies
ICAR said in a statement:
The development is expected to accelerate the breeding of climate-resilient, high-yielding and nutritionally enriched pigeonpea varieties, thereby strengthening the country's pulse improvement programme. The achievement will provide a major impetus to research and innovation, benefit scientists, breeders and farmers, and contribute to enhanced productivity, improved farmer livelihoods, and India's food and nutritional security.
The announcement coincides with the launch of the Mission for 'Aatmanirbharta in Pulses' (2025-26 to 2030-31) to achieve self-sufficiency in pulse production, according to ICAR. In July, Union Agriculture Minister Shivraj Singh Chouhan called upon the scientific community to look for non-genetically modified organism (non-GMO) solutions to raise productivity in pulses. “If countries without access to GM seeds can get better yields in pulses, why can’t India?” Chouhan had said at the 98th Foundation Day of ICAR.
The genome resource is positioned by ICAR to strengthen India's pulse improvement programme and support the national pulse self-sufficiency mission running from 2025-26 to 2030-31, providing a long-term reference for breeders working to lift pigeonpea productivity.
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