Telomere-to-telomere genome assemblies and population resequencing of diploid and allotetraploid peanut varieties
Peanut (Arachis hypogaea L.) is a globally significant leguminous oil crop. Here we present telomere-to-telomere genome assemblies for two diploid and four tetraploid peanut varieties, resulting in high-quality reference genomes, showing that the complex activities of transposable elements, chromosomal rearrangements and centromere expansions within subgenomes collectively contribute to the asymmetrical evolution of the tetraploid genome, and unique structural variants in the four tetraploid peanut varieties provide clear evidence of domestication. Population analyses of 521 peanut accessions revealed asymmetric selection events between subgenomes during breeding, and genome-wide association studies identified candidate genes linked to oil content, seed size and weight, kernel dehydration rate, and arachidic acid content. In addition, transcriptomic and metabolomic analyses revealed enhanced activity in lipidomic and anthocyanin biosynthetic pathways during seed development. These comprehensive findings provide insights into genome organization, evolutionary dynamics and phenotypic differentiation across peanut varieties that could inform future peanut breeding and improvement strategies.
Authors
- Xing Wang Deng (ORCID: https://orcid.org/0000-0001-8709-1467)
- Rajeev Kumar Varshney (ORCID: https://orcid.org/0000-0002-4562-9131)
- Annapurna Chitikineni (ORCID: https://orcid.org/0000-0002-1058-2900)
- Yilin Zhang (ORCID: https://orcid.org/0000-0002-4273-1851)
- Yuan Lv (ORCID: https://orcid.org/0000-0003-1260-5800)
- Jianxin Bian (ORCID: https://orcid.org/0000-0001-6443-7218)
- Vanika Garg (ORCID: https://orcid.org/0000-0001-6446-4603)
- 唐荣华
- Chuanzhi Zhao (ORCID: https://orcid.org/0000-0001-7465-7425)
- Liangsheng Zhang (ORCID: https://orcid.org/0000-0003-1919-3677)
- X Wang
- Liangqiong He (ORCID: https://orcid.org/0000-0002-4699-304X)
- Haosong Guo
- Shuai Ding (ORCID: https://orcid.org/0009-0008-9803-3754)
- Yu Guan (ORCID: https://orcid.org/0000-0002-5297-7273)
- H. He (ORCID: https://orcid.org/0009-0008-3906-2037)
- Xiaoqin Liu (ORCID: https://orcid.org/0000-0001-9232-3461)
- Yuanyuan Cui
- Jihua Li
- Qingjing Meng
- Guoliang Zhou
- Tianyu Li
- Kui Li
Institutions
- Murdoch University (AU)
- Yangtze River Delta Physics Research Center (China) (CN)
- Shandong Academy of Agricultural Sciences (CN)
- Guangxi Academy of Agricultural Science (CN)
- Center for Life Sciences (CN)
- Zhejiang University of Technology (CN)
- Weifang University (CN)
Publication Details
- Journal
- Nature Genetics
- Published
- 2026-04-24
- DOI
- https://doi.org/10.1038/s41588-026-02577-z
- Primary Topic
- Peanut Plant Research Studies
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Murdoch University
- Natural Science Foundation of Shandong Province
- Peking University