J Integr Plant Biol

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  • 收稿日期:2025-09-15 接受日期:2026-05-02

High‐quality genome of elite peanut cultivar ZH05 reveals subgenome asymmetry, pan‐genome diversity, and breeding insights

Taihua Yang1,2, Nian Liu1, Li Huang1, Jianbin Guo1, Xiaomeng Xue1,2, Mingjun Wang1, Xiaohan Zhang2, Chengtao Quan2,3, Enyou Feng4, Jiazhuang Tan4, Zhenzhen Zhang5, Yu You5, Youlin Xia5, Dongxin Huai1, Yuning Chen1, Liyin Yan1, Kede Liu2, Huifang Jiang1*, Yong Lei1* and Boshou Liao1*   

  1. 1. Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI‐CAAS), Wuhan 430062, China
    2. National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
    3. Biobreeding Institute, Xianghu Laboratory, Hangzhou 311231, China
    4. Zhanjiang Academy of Agricultural Sciences, Zhanjiang 524000, China
    5. Nanchong Academy of Agricultural Sciences, Nanchong 637000, China
    *Correspondences: Boshou Liao (lboshou@hotmail.com, Dr. Liao is fully responsible for the distribution of all materials associated with this article); Yong Lie (leiyong@caas.cn); Huifang Jiang (peanutlab@oilcrops.cn)
  • Received:2025-09-15 Accepted:2026-05-02
  • Supported by:
    This work was supported by the National Key Research and Development Program of China (2022YFD1200400), the National Peanut Industry Technology System Construction (CARS‐13), the National Crop Germplasm Resources Center (NCGRC‐2025‐036), the National Program for Crop Germplasm Protection of China (19210163), and the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences (CAAS‐ASTIP‐2024‐OCRI).

Abstract: Peanut (Arachis hypogaea) is an allotetraploid legume crop of agricultural and economic importance worldwide. Despite advances in peanut genomics, the integration of genetic diversity with multi-omics landscapes remains limited, and a comprehensive understanding of subgenome asymmetry is still lacking. Here, we present a high-quality genome assembly of an elite peanut cultivar Zhonghua 5 (ZH05; 2,622.85 Mb with 73,718 predicted genes) and construct a species-specific pan-genome based on 1,286 accessions, uncovering 849.82 Mb of non-reference sequences and 18,484 novel genes. Over 23 million genetic variants and extensive gene PAVs substantially expand the landscape of genetic diversity in peanut. Integrative multi-omics (transcriptome, DNA methylation, chromatin accessibility, and three-dimensional genome architecture), combined with population genomics analyses, reveal pronounced and multi-layered subgenome asymmetry. Specifically, SubA shows higher chromatin accessibility and overall gene expression, whereas SubB displays more transposable elements, elevated DNA methylation, more genes under selection during domestication, and stronger three-dimensional chromatin interactions with more stable topologically associating domains. Furthermore, genetic dissection using a recombinant inbred line population identified several major stable QTLs for seed size, whose pyramiding contributes to ZH05's superior yield performance. Collectively, this study establishes an integrated genomic framework for peanut, illuminates asymmetric subgenome evolution across sequence, epigenetic, and chromatin architecture, and provides valuable resources for accelerating molecular breeding and crop improvement.

Key words: Arachis hypogaea, genome assembly, multi-omics, pan-genome, QTL mapping, subgenome asymmetry

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