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

文献类型： 外文期刊

第一作者： Zhao, Kunkun

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

作者机构：

期刊名称：NATURE GENETICS （ 影响因子：29.0； 五年影响因子：37.4 ）

ISSN： 1061-4036

年卷期： 2025 年 57 卷 5 期

页码：

收录情况： SCI

摘要： 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.

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