Origin and de novo domestication of sweet orange
Sweet orange is cultivated worldwide but suffers from various devastating diseases because of its monogenetic background. The elucidation of the origin of a crop facilitates the domestication of new crops that may better cope with new challenges. Here we collected and sequenced 226 citrus accessions and assembled telomere-to-telomere phased diploid genomes of sweet orange and sour orange. On the basis of a high-resolution haplotype-resolved genome analysis, we inferred that sweet orange originated from a sour orange × mandarin cross and confirmed this model using artificial hybridization experiments. We identified defense-related metabolites that potently inhibited the growth of multiple industrially important pathogenic bacteria. We introduced diversity to sweet orange, which showed wide segregation in fruit flavor and disease resistance and produced canker-resistant sweet orange by selecting defense-related metabolites. Our findings elucidate the origin of sweet orange and de novo domesticated disease-resistant sweet oranges, illuminating a strategy for the rapid domestication of perennial crops.
Authors
- Wen‐Biao Jiao (ORCID: https://orcid.org/0000-0001-8355-2959)
- Robert M. Larkin
- Zongzhou Xie (ORCID: https://orcid.org/0000-0001-7971-8565)
- Yue Huang (ORCID: https://orcid.org/0000-0002-6572-2341)
- Kun Yang (ORCID: https://orcid.org/0000-0002-0907-5047)
- Yanjun Zan (ORCID: https://orcid.org/0000-0001-5571-4578)
- Wen‐Wu Guo (ORCID: https://orcid.org/0000-0002-2519-9672)
- Zhihao Lü (ORCID: https://orcid.org/0000-0001-9091-4946)
- Qiang Xu (ORCID: https://orcid.org/0000-0003-1786-9696)
- Pengfei Wan (ORCID: https://orcid.org/0000-0003-0140-4990)
- Weikang Zheng (ORCID: https://orcid.org/0000-0003-0106-9360)
- Lijun Chai (ORCID: https://orcid.org/0000-0001-7896-3729)
- Fang Ding (ORCID: https://orcid.org/0000-0002-9697-7179)
- Xiuxin Deng (ORCID: https://orcid.org/0000-0003-4490-4514)
- Peng Chen (ORCID: https://orcid.org/0000-0001-8024-1813)
- Junli Ye (ORCID: https://orcid.org/0000-0002-2976-7585)
- Yuantao Xu
- Guanglian Liao (ORCID: https://orcid.org/0000-0002-8949-630X)
- Junjie Liu (ORCID: https://orcid.org/0000-0002-8982-107X)
- Xia Wang (ORCID: https://orcid.org/0000-0002-7750-1167)
- Fei Zhang (ORCID: https://orcid.org/0009-0002-9879-5165)
- Xin D. Gao (ORCID: https://orcid.org/0000-0002-7108-3574)
- Shulin Chen (ORCID: https://orcid.org/0000-0002-0280-1536)
- Shengjun Liu (ORCID: https://orcid.org/0009-0004-8321-3585)
- Fa He (ORCID: https://orcid.org/0000-0002-1843-016X)
- Zhiyong Pan (ORCID: https://orcid.org/0000-0002-0018-4298)
- Lun Wang (ORCID: https://orcid.org/0000-0002-9429-6599)
- Zishuang Liu
- Gong‐Ao Xiao
- Xiuli Zeng
- Zongcheng Lin
Institutions
- Huazhong Agricultural University (CN)
- Wuhan University (CN)
- Tobacco Research Institute (CN)
- Hunan Academy of Agricultural Sciences (CN)
- Shanghai Zhangjiang Laboratory (CN)
- Chinese Academy of Agricultural Sciences (CN)
- Ministry of Agriculture and Rural Affairs (CN)
Publication Details
- Journal
- Nature Genetics
- Published
- 2025-03-01
- DOI
- https://doi.org/10.1038/s41588-025-02122-4
- Citations
- 13
- Primary Topic
- Horticultural and Viticultural Research
- Type
- article
- Field-Weighted Citation Impact
- 22.75
Funders
- Huazhong Agricultural University
- Hunan Agricultural University