Phenotypic and genomic signatures across wild Rosa species open new horizons for modern rose breeding

Bixuan Cheng; Kai Zhao; Meichun Zhou; Peter M. Bourke; Lijun Zhou; Sihui Wu; Yanlin Sun; Lifang Geng; Wenting Du; Chenyang Yang; Juntong Chen; Runhuan Huang; Xiaoling Tian; Lei Zhang; He Huang; Yu Han; Huitang Pan; Qixiang Zhang; Le Luo; Chao Yu

doi:10.1038/s41477-025-01955-5

Phenotypic and genomic signatures across wild Rosa species open new horizons for modern rose breeding

Bixuan Cheng, Kai Zhao, Meichun Zhou, Peter M. Bourke, Lijun Zhou, Sihui Wu, Yanlin Sun, Lifang Geng, Wenting Du, Chenyang Yang, Juntong Chen, Runhuan Huang, Xiaoling Tian, Lei Zhang, He Huang, Yu Han, Huitang Pan, Qixiang Zhang, Le Luo, Chao Yu^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

2 Citations (Scopus)

Abstract

The cultivation and domestication of roses reflects cultural exchanges and shifts in aesthetics that have resulted in today’s most popular ornamental plant group. However, the narrow genetic foundation of cultivated roses limits their further improvement. Wild Rosa species harbour vast genetic diversity, yet their utilization is impeded by taxonomic confusion. Here we generated a phased and gap-free reference genome of Rosa persica for phylogenetic and population genomic analyses of a large collection of Rosa samples. The robust nuclear and plastid phylogenies support most of the morphology-based traditional taxonomy of Rosa. Population genomic analyses disclosed potential genetic exchanges among sections, indicating the northwest and southwest of China as two independent centres of diversity for Rosa. Analyses of domestication traits provide insights into selection processes related to flower colour, fragrance, double flower and resistance. This study provides a comprehensive understanding of rose domestication and lays a solid foundation for future re-domestication and innovative breeding efforts using wild resources.

Original language	English
Pages (from-to)	775-789
Number of pages	15
Journal	Nature Plants
Volume	11
DOIs	https://doi.org/10.1038/s41477-025-01955-5
Publication status	Published - Apr 2025

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Cheng, B., Zhao, K., Zhou, M., Bourke, P. M., Zhou, L., Wu, S., Sun, Y., Geng, L., Du, W., Yang, C., Chen, J., Huang, R., Tian, X., Zhang, L., Huang, H., Han, Y., Pan, H., Zhang, Q., Luo, L., & Yu, C. (2025). Phenotypic and genomic signatures across wild Rosa species open new horizons for modern rose breeding. Nature Plants, 11, 775-789. https://doi.org/10.1038/s41477-025-01955-5

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title = "Phenotypic and genomic signatures across wild Rosa species open new horizons for modern rose breeding",

abstract = "The cultivation and domestication of roses reflects cultural exchanges and shifts in aesthetics that have resulted in today{\textquoteright}s most popular ornamental plant group. However, the narrow genetic foundation of cultivated roses limits their further improvement. Wild Rosa species harbour vast genetic diversity, yet their utilization is impeded by taxonomic confusion. Here we generated a phased and gap-free reference genome of Rosa persica for phylogenetic and population genomic analyses of a large collection of Rosa samples. The robust nuclear and plastid phylogenies support most of the morphology-based traditional taxonomy of Rosa. Population genomic analyses disclosed potential genetic exchanges among sections, indicating the northwest and southwest of China as two independent centres of diversity for Rosa. Analyses of domestication traits provide insights into selection processes related to flower colour, fragrance, double flower and resistance. This study provides a comprehensive understanding of rose domestication and lays a solid foundation for future re-domestication and innovative breeding efforts using wild resources.",

author = "Bixuan Cheng and Kai Zhao and Meichun Zhou and Bourke, {Peter M.} and Lijun Zhou and Sihui Wu and Yanlin Sun and Lifang Geng and Wenting Du and Chenyang Yang and Juntong Chen and Runhuan Huang and Xiaoling Tian and Lei Zhang and He Huang and Yu Han and Huitang Pan and Qixiang Zhang and Le Luo and Chao Yu",

year = "2025",

month = apr,

doi = "10.1038/s41477-025-01955-5",

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journal = "Nature Plants",

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T1 - Phenotypic and genomic signatures across wild Rosa species open new horizons for modern rose breeding

AU - Cheng, Bixuan

AU - Zhao, Kai

AU - Zhou, Meichun

AU - Bourke, Peter M.

AU - Zhou, Lijun

AU - Wu, Sihui

AU - Sun, Yanlin

AU - Geng, Lifang

AU - Du, Wenting

AU - Yang, Chenyang

AU - Chen, Juntong

AU - Huang, Runhuan

AU - Tian, Xiaoling

AU - Zhang, Lei

AU - Huang, He

AU - Han, Yu

AU - Pan, Huitang

AU - Zhang, Qixiang

AU - Luo, Le

AU - Yu, Chao

PY - 2025/4

Y1 - 2025/4

N2 - The cultivation and domestication of roses reflects cultural exchanges and shifts in aesthetics that have resulted in today’s most popular ornamental plant group. However, the narrow genetic foundation of cultivated roses limits their further improvement. Wild Rosa species harbour vast genetic diversity, yet their utilization is impeded by taxonomic confusion. Here we generated a phased and gap-free reference genome of Rosa persica for phylogenetic and population genomic analyses of a large collection of Rosa samples. The robust nuclear and plastid phylogenies support most of the morphology-based traditional taxonomy of Rosa. Population genomic analyses disclosed potential genetic exchanges among sections, indicating the northwest and southwest of China as two independent centres of diversity for Rosa. Analyses of domestication traits provide insights into selection processes related to flower colour, fragrance, double flower and resistance. This study provides a comprehensive understanding of rose domestication and lays a solid foundation for future re-domestication and innovative breeding efforts using wild resources.

AB - The cultivation and domestication of roses reflects cultural exchanges and shifts in aesthetics that have resulted in today’s most popular ornamental plant group. However, the narrow genetic foundation of cultivated roses limits their further improvement. Wild Rosa species harbour vast genetic diversity, yet their utilization is impeded by taxonomic confusion. Here we generated a phased and gap-free reference genome of Rosa persica for phylogenetic and population genomic analyses of a large collection of Rosa samples. The robust nuclear and plastid phylogenies support most of the morphology-based traditional taxonomy of Rosa. Population genomic analyses disclosed potential genetic exchanges among sections, indicating the northwest and southwest of China as two independent centres of diversity for Rosa. Analyses of domestication traits provide insights into selection processes related to flower colour, fragrance, double flower and resistance. This study provides a comprehensive understanding of rose domestication and lays a solid foundation for future re-domestication and innovative breeding efforts using wild resources.

U2 - 10.1038/s41477-025-01955-5

DO - 10.1038/s41477-025-01955-5

M3 - Article

AN - SCOPUS:105001983979

SN - 2055-026X

VL - 11

SP - 775

EP - 789

JO - Nature Plants

JF - Nature Plants

ER -

Phenotypic and genomic signatures across wild Rosa species open new horizons for modern rose breeding

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