In a major milestone for India’s agricultural biotechnology programme, the Indian Council of Agricultural Research (ICAR) has developed the country’s first fully annotated telomere-to-telomere (T2T) reference genome of pigeonpea (Cajanus cajan), a breakthrough expected to accelerate the development of high-yielding, climate-resilient and nutritionally superior pulse varieties.
Pigeonpea, popularly known as tur or arhar, is one of India’s most important pulse crops and a key source of dietary protein, making it central to the country’s food and nutritional security.
The latest achievement builds on ICAR–National Institute for Plant Biotechnology’s (NIPB), New Delhi, pioneering work in pigeonpea genomics. In 2011, the institute published the world’s first draft genome of a pulse crop using the pigeonpea variety ‘Asha’—also the first crop genome to be sequenced entirely in India. An improved version followed in 2017, while the newly completed telomere-to-telomere genome provides the most comprehensive genetic blueprint of the crop to date.
Complete genetic map
The newly developed genome comprises 752.65 million base pairs of DNA 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 National Center for Biotechnology Information (NCBI) database under accession number GCF_000230855.1 and was officially released on April 20, 2026.
The assembly captures all 11 centromeres and 22 telomeres, demonstrating chromosome-level completeness. Researchers identified 36,557 genes, generating 48,008 messenger RNA (mRNA) coding sequences. Transcriptome mapping recorded more than 99.9% read alignment, highlighting the genome’s exceptional accuracy and completeness.
Boost for pulse research
ICAR said the fully annotated T2T reference genome will become a valuable national genomic resource, enabling advanced gene discovery, pangenome analysis, molecular breeding and genome-editing research.
The genomic resource is expected to help scientists identify genes associated with key agronomic traits such as higher yield, disease resistance, climate resilience and improved nutritional quality, significantly reducing the time required to develop improved pigeonpea varieties.
The breakthrough is expected to strengthen India’s pulse improvement programme while providing a major boost to agricultural biotechnology research, benefiting scientists, plant breeders and farmers alike.
Supporting self-reliance in pulses
The development comes as the Government of India intensifies efforts to reduce dependence on pulse imports through the Mission for Aatmanirbharta in Pulses, which runs from 2025-26 to 2030-31.
The mission aims to raise India’s pulse production to around 35 million tonnes by 2030-31 through improved seed varieties, technology adoption, expansion of cultivation, assured procurement and stronger post-harvest infrastructure.
ICAR continues to play a central role in the programme by developing high-yielding, pest-resistant and climate-resilient pulse varieties, producing breeder seeds, conducting multi-location field trials and promoting modern cultivation practices through its research institutes and Krishi Vigyan Kendras (KVKs).
The successful decoding of India’s first complete pigeonpea genome is expected to significantly strengthen these efforts by providing researchers with an invaluable genomic roadmap for developing the next generation of pulse varieties capable of meeting the country’s growing food and nutritional requirements.