Pangenome analysis reveals structural variation associated with seed size and weight traits in peanut

Kunkun Zhao; Hongzhang Xue; Guowei Li; Annapurna Chitikineni; Yi Fan; Zenghui Cao; Xiaorui Dong; Huimin Lu; Kai Zhao; Lin Zhang; Ding Qiu; Rui Ren; Fangping Gong; Zhongfeng Li; Xingli Ma; Shubo Wan; Rajeev K Varshney; Chaochun Wei; Dongmei Yin

doi:10.1038/s41588-025-02170-w

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Pangenome analysis reveals structural variation associated with seed size and weight traits in peanut

Journal article

Open access

Peer reviewed

Pangenome analysis reveals structural variation associated with seed size and weight traits in peanut

Kunkun Zhao, Hongzhang Xue, Guowei Li, Annapurna Chitikineni, Yi Fan, Zenghui Cao, Xiaorui Dong, Huimin Lu, Kai Zhao, Lin Zhang, …

Nature genetics, Vol.57, pp.1250-1261

2025

DOI: https://doi.org/10.1038/s41588-025-02170-w

PMID: 40295880

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Abstract

Peanut (Arachis hypogaea L.) is an important oilseed and food legume crop, with seed size and weight being critical traits for domestication and breeding. However, genomic rearrangements like structural variations (SVs) underlying seed size and weight remain unclear. Here we present a comprehensive pangenome analysis utilizing eight high-quality genomes (two diploid wild, two tetraploid wild and four tetraploid cultivated peanuts) and resequencing data of 269 accessions with diverse seed sizes. We identified 22,222 core or soft-core, 22,232 distributed and 5,643 private gene families. The frequency of SVs in subgenome A is higher than in subgenome B. We identified 1,335 domestication-related SVs and 190 SVs associated with seed size or weight. Notably, a 275-bp deletion in gene AhARF2-2 results in loss of interaction with AhIAA13 and TOPLESS, reducing the inhibitory effect on AhGRF5 and promoting seed expansion. This high-quality pangenome serves as a fundamental resource for the genetic enhancement of peanuts and other legume crops.

Details

Title: Pangenome analysis reveals structural variation associated with seed size and weight traits in peanut
Authors/Creators: Kunkun Zhao - Henan Agricultural University
Hongzhang Xue - Henan Agricultural University
Guowei Li - Shandong Normal University
Annapurna Chitikineni - Murdoch University
Yi Fan - Henan Agricultural University
Zenghui Cao - Henan Agricultural University
Xiaorui Dong - Shanghai Jiao Tong University
Huimin Lu - Shanghai Jiao Tong University
Kai Zhao - Henan Agricultural University
Lin Zhang - Henan Agricultural University
Ding Qiu - Henan Agricultural University
Rui Ren - Henan Agricultural University
Fangping Gong - Henan Agricultural University
Zhongfeng Li - Henan Agricultural University
Xingli Ma - Henan Agricultural University
Shubo Wan - Shandong Academy of Agricultural Sciences
Rajeev K Varshney - Murdoch University, Food Futures Institute
Chaochun Wei - Shanghai Jiao Tong University
Dongmei Yin - Henan Agricultural University
Publication Details: Nature genetics, Vol.57, pp.1250-1261
Publisher: Springer Nature
Number of pages: 21
Identifiers: 991005779333607891
Murdoch Affiliation: Centre for Crop and Food Innovation; State Agricultural Biotechnology Centre; Food Futures Institute
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.54 Molecular & Cell Biology - Genetics; 1.54.1543 Flow Cytometry
Web Of Science research areas: Genetics & Heredity
ESI research areas: Molecular Biology & Genetics