Researchers from the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), in collaboration with leading agricultural research institutions in China and Australia, have conducted the most comprehensive genomic investigation of cultivated peanut, uncovering previously hidden genetic diversity that could accelerate global groundnut improvement.
Published in Nature Genetics, the study, titled “Pan-genome-based resequencing of 2,320 accessions reveals structural variations and accelerates breeding advances in cultivated peanut,” analysed 2,320 peanut accessions from 87 countries, providing an unprecedented genomic resource for researchers and plant breeders worldwide.
The research was co-led by Dr Manish K. Pandey, Principal Scientist – Genebank and Trait Discovery at ICRISAT’s Centre for Pre-breeding Research (CPBR), alongside scientists from the Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences (SAAS), Jinan, China; the State Agricultural Biotechnology Centre (SABC), Murdoch University, Australia; and the Henan Academy of Agricultural Sciences, Zhengzhou, China.
Drawing on genetic resources conserved in ICRISAT’s Genebank, the study analysed material representing 88.03 per cent of ICRISAT’s core collection and 59.21 per cent of the United States Department of Agriculture (USDA) peanut collection.
“Pan-genome studies are important for advancing global agricultural research. ICRISAT’s genomics research and Genebank have made significant contributions to pan-genome studies in important pulses, including chickpea and pigeonpea. This latest publication in Nature Genetics on the peanut pan-genome is another key milestone towards delivering improved crops for smallholder farmers in the drylands,” said Dr Himanshu Pathak, Director General, ICRISAT.
The research identified previously undetected structural variations (SVs) and homoeologous exchanges across the peanut genome, offering new insights into the crop’s genetic architecture.
It also identified genes associated with important agricultural traits, including AhTFL1, which is linked to flowering-time regulation, and Ah12g032500, identified as a dwarfing gene.
The findings could support the development of improved groundnut varieties with desirable characteristics. Dwarf plant architecture, for instance, can facilitate mechanised harvesting and allow higher planting densities, potentially improving production efficiency and strengthening climate resilience.
The genomic resource also creates opportunities to identify superior genetic variants associated with traits such as seed size and pod number.
“Pan-genome assemblies require strong international cooperation. I congratulate the collaborating institutions in China and Murdoch University, alongside ICRISAT’s Centre for Pre-breeding Research, on this remarkable achievement. Such partnerships are essential to advancing crop science and translating genomic discoveries into practical breeding outcomes,” said Dr Stanford Blade, Deputy Director General – Research and Innovation, ICRISAT.
Dr Raman Babu, Global Research Program Director – Accelerated Crop Improvement, ICRISAT, said the institute’s Genebank played a central role in the discovery.
“ICRISAT’s Genebank is at the heart of this discovery. Identifying genes associated with traits such as flowering-time regulation and dwarfing provides valuable resources for breeding climate-resilient groundnut varieties. This study demonstrates how conserved genetic diversity can be leveraged for breeding better varieties that benefit the farmers,” he said.
Highlighting the broader implications for global breeding programmes, Dr Pandey said: “For decades, groundnut breeding has faced challenges associated with a narrow genetic base. This graph-based pan-genome captures structural variations that are important for crop improvement. This public resource can help accelerate the development of high-yielding, nutritionally superior and climate-resilient groundnut varieties across the globe.”
The study marks a significant advance in peanut genomics, demonstrating the importance of international scientific collaboration and long-term investment in germplasm conservation.
By making a comprehensive genomic resource available to the global research community, it provides a stronger foundation for developing productive, resilient and farmer-preferred groundnut varieties for agricultural systems worldwide.
