Origin and de novo domestication of sweet orange. Liu, S., Xu, Y., Yang, K., Huang, Y., Lu, Z., Chen, S., Gao, X., Xiao, G., Chen, P., Zeng, X., Wang, L., Zheng, W., Liu, Z., Liao, G., He, F., Liu, J., Wan, P., Ding, F., Ye, J., Jiao, W., Chai, L., Pan, Z., Zhang, F., Lin, Z., Zan, Y., Guo, W., Larkin, R. M., Xie, Z., Wang, X., Deng, X., & Xu, Q. Nature Genetics, 57(3):754–762, Nature Publishing Group, March, 2025.
Origin and de novo domestication of sweet orange [link]Paper  doi  abstract   bibtex   
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.
@article{liu_origin_2025,
	title = {Origin and de novo domestication of sweet orange},
	volume = {57},
	copyright = {2025 The Author(s)},
	issn = {1546-1718},
	url = {https://www.nature.com/articles/s41588-025-02122-4},
	doi = {10.1038/s41588-025-02122-4},
	abstract = {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.},
	language = {en},
	number = {3},
	urldate = {2026-05-19},
	journal = {Nature Genetics},
	publisher = {Nature Publishing Group},
	author = {Liu, Shengjun and Xu, Yuantao and Yang, Kun and Huang, Yue and Lu, Zhihao and Chen, Shulin and Gao, Xiang and Xiao, Gongao and Chen, Peng and Zeng, Xiuli and Wang, Lun and Zheng, Weikang and Liu, Zishuang and Liao, Guanglian and He, Fa and Liu, Junjie and Wan, Pengfei and Ding, Fang and Ye, Junli and Jiao, Wenbiao and Chai, Lijun and Pan, Zhiyong and Zhang, Fei and Lin, Zongcheng and Zan, Yanjun and Guo, Wenwu and Larkin, Robert M. and Xie, Zongzhou and Wang, Xia and Deng, Xiuxin and Xu, Qiang},
	month = mar,
	year = {2025},
	keywords = {Plant breeding, Plant genetics, Plant molecular biology},
	pages = {754--762},
}
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