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

Nature Plants volume 11, pages 775–789 (2025)Cite this article

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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.

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Fig. 1: Geographical distribution of core Rosa accessions.
Fig. 2: Phylogenetic relationships of 215 Rosa accessions based on 6,048 SNPs of 707 single-copy nuclear genes.
Fig. 3: Ancestral state reconstruction of the four selected traits of Rosa, performed using both the maximum parsimony method (at the node of the tree) and the maximum likelihood method (above the node of the tree) for the backbone of the single-copy SNP tree.
Fig. 4: Population structure of Rosa accessions.
Fig. 5: Demographic history of Rosa.
Fig. 6: Genome-wide identification and selective sweep analysis across Rosa populations.

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Data availability

Raw sequencing data have been deposited in the National Center for Biotechnology Information (NCBI) BioProject database with the BioProject PRJNA1224503. The phased genome assembly of R. persica has been deposited in the NCBI database under accession numbers JBLIYO000000000 (Hap 1) and JBLIYP000000000 (Hap 2). The previously published reads used in this study are available from NCBI and public GDR database at https://www.rosaceae.org. Specific source data are listed in Supplementary Tables 10 and 13.

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Acknowledgements

We thank Y. Yang (Kunming Yang Chinese Rose Gardening) for collecting wild Rosa resources and for helpful discussions on Rosa taxonomy. We are grateful to Y. Sui and R. Guo (Xinjiang Career Technical College) for their efforts in collecting Rosa resources in Xinjiang. We thank X. Gao (Key Laboratory of Molecular Epigenetics of Ministry of Education (MOE), Northeast Normal University) for his inspiring discussion and comments. We appreciate the valuable suggestions on the manuscript provided by R. Smulders and P. Arens (Plant Breeding, Wageningen University and Research). We thank J. Endelman (University of Wisconsin) for his instruction on GWASpoly software. We thank Man Zhang and T. Zheng for the suggestions on improving the paper. We thank J. Zhao (Boyce Thompson Institute) for his instruction on demographic analyses. We thank Yuxuan Zhang, L. Ji, Yujing Zhang, L. Jiang, C. Feng, Y. Zhuang, Z. Ou, R. Wang, J. Tang and K. Xiong for their assistance with the investigations of Rosa species. Furthermore, we thank Wuhan Dazhong Yuansheng Technology, Wuhan Feisha Genetic Information (www.frasergen.com) and BerryGenomics (www.berrygenomics.com) for providing essential sequencing service. Finally, the authors are profoundly indebted to every member of the Fishpond family, whose collective efforts were instrumental in the fruition of this work. This research was supported by the Fundamental Research Funds for the Central Universities (grant number QNTD202306 to C. Yu), National Key R&D Program of China (grant number 2019YFD1000400 to C. Yu) and National Natural Science Foundation of China (grant numbers 32471955 and 32071818 to C. Yu).

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Authors and Affiliations

  1. State Key Laboratory of Efficient Production of Forest Resources, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture and School of Landscape Architecture, Beijing Forestry University, Beijing, China

    Bixuan Cheng, Meichun Zhou, Lijun Zhou, Sihui Wu, Yanlin Sun, Lifang Geng, Wenting Du, Chenyang Yang, Runhuan Huang, Xiaoling Tian, Lei Zhang, He Huang, Yu Han, Huitang Pan, Qixiang Zhang, Le Luo & Chao Yu

  2. College of Life Sciences, Fujian Normal University, Fuzhou, China

    Kai Zhao

  3. Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands

    Peter M. Bourke

  4. Key Laboratory of Plant Diversity and Specialty Crops, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China

    Juntong Chen

Authors
  1. Bixuan Cheng
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  2. Kai Zhao
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  3. Meichun Zhou
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  4. Peter M. Bourke
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  5. Lijun Zhou
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  6. Sihui Wu
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  7. Yanlin Sun
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  8. Lifang Geng
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  9. Wenting Du
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  10. Chenyang Yang
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  11. Juntong Chen
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  12. Runhuan Huang
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  13. Xiaoling Tian
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  14. Lei Zhang
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  15. He Huang
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  16. Yu Han
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  17. Huitang Pan
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  18. Qixiang Zhang
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  19. Le Luo
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  20. Chao Yu
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Contributions

C. Yu designed and managed the project. B.C. performed population genomic analyses and wrote the manuscript. K.Z. assembled the Rosa persica genome and performed genomic analyses. M.Z. performed GWAS analysis. P.M.B. provided guidance on GWAS analysis and revised the manuscript. L. Zhou and Y.S. managed the plant materials. S.W. performed population history analyses. L.G. performed selective sweep analyses. W.D. performed demographic analyses. C. Yang and J.C. constructed phylogenetic trees and performed phylogenetic analyses. R.H. designed and revised the figures. X.T. performed karyotype analyses of Rosa materials. L. Zhang performed data analyses. C. Yu, B.C., K.Z., M.Z., L.G., W.D. and S.W. wrote the paper with contributions from H.H., Y.H., L.L., H.P. and Q.Z.

Corresponding author

Correspondence to Chao Yu.

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Nature Plants thanks Xingtan Zhang and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data

Extended Data Fig. 1 Flower traits of Rosa accessions used in this study.

The plates of accessions are sorted by scientific groups. Sample IDs correspond to Supplementary Table 13.

Extended Data Fig. 2 Leaf traits of Rosa accessions used in this study.

The plates of accessions are sorted by number of leaflets. Sample IDs correspond to Supplementary Table 13.

Extended Data Fig. 3 Comparison between plastid phylogeny (left) based on chloroplast coding sequences, and nuclear phylogeny (right) based on single-copy SNPs.

Both trees were constructed using maximum likelihood method. Bootstrap values were tested with 1,000 replicates. The colors represent accessions from different botanical groups, in correspondence with previous figures.

Extended Data Fig. 4 Geographical distributions of different botanical sections of Rosa.

The white dots represent distribution information of Rosa accessions, which was derived from field investigation, specimen information, and geographic distribution records from Flora of China and Chinese Virtual Herbarium (http://www.cvh.ac.cn).

Supplementary information

Supplementary Information (download PDF )

Supplementary Figs. 1–12, notes and methods.

Reporting Summary (download PDF )

Supplementary Tables (download XLSX )

Supplementary Tables 1–20.

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Cheng, B., Zhao, K., Zhou, M. et al. Phenotypic and genomic signatures across wild Rosa species open new horizons for modern rose breeding. Nat. Plants 11, 775–789 (2025). https://doi.org/10.1038/s41477-025-01955-5

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