High‐quality genome of elite peanut cultivar ZH05 reveals subgenome asymmetry, pan‐genome diversity, and breeding insights
5 affiliations
- 1Key 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
- 2National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology Huazhong Agricultural University Wuhan 430070 China
- 3Biobreeding Institute Xianghu Laboratory Hangzhou 311231 China
- 4Zhanjiang Academy of Agricultural Sciences Zhanjiang 524000 China
- 5Nanchong Academy of Agricultural Sciences Nanchong 637000 China
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.
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BibTeX
@article{yang2026highquality,
title = {{High‐quality genome of elite peanut cultivar ZH05 reveals subgenome asymmetry, pan‐genome diversity, and breeding insights}},
author = {Taihua Yang and Nian Liu and Li Huang and Jianbin Guo and Xiaomeng Xue and Mingjun Wang and Xiaohan Zhang and Chengtao Quan and Enyou Feng and Jiazhuang Tan and Zhenzhen Zhang and Yu You and Youlin Xia and Dongxin Huai and Yuning Chen and Liying Yan and Kede Liu and Huifang Jiang and Yong Lei and Boshou Liao},
journal = {Journal of Integrative Plant Biology},
year = {2026},
month = jun,
doi = {10.1111/jipb.70308},
url = {https://doi.org/10.1111/jipb.70308},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - High‐quality genome of elite peanut cultivar ZH05 reveals subgenome asymmetry, pan‐genome diversity, and breeding insights
AU - Taihua Yang
AU - Nian Liu
AU - Li Huang
AU - Jianbin Guo
AU - Xiaomeng Xue
AU - Mingjun Wang
AU - Xiaohan Zhang
AU - Chengtao Quan
AU - Enyou Feng
AU - Jiazhuang Tan
AU - Zhenzhen Zhang
AU - Yu You
AU - Youlin Xia
AU - Dongxin Huai
AU - Yuning Chen
AU - Liying Yan
AU - Kede Liu
AU - Huifang Jiang
AU - Yong Lei
AU - Boshou Liao
PY - 2026
DA - 2026/06/01
JO - Journal of Integrative Plant Biology
DO - 10.1111/jipb.70308
UR - https://doi.org/10.1111/jipb.70308
AB - 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.
SN - 1672-9072
SN - 1744-7909
ER -