Abstract
Polyploidization is a common and important evolutionary process in the plant kingdom. Compared with diploid plant species, the intricate genome architecture of polyploid plant species presents substantial challenges in applying multi-omics approaches for crop breeding improvement. In this Review, we summarize the current techniques for analysing polyploid genomes, including constructing reference genomes and pan-genomes, and detecting variants. We also assess findings related to polyploid genome architecture, population genetics and breeding programmes, highlighting advanced techniques in the breeding of polyploid crops. Finally, we explore the challenges and demands posed by polyploid genome complexity during analysis with available biotechnological tools. This Review emphasizes the importance of a comprehensive understanding of polyploid genomic features for the further genetic improvement of polyploid crops.
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Acknowledgements
The assembled polyploid genomes in Fig. 1 are based on our own compilation from publicly available resources, primarily the PubPlant database, which may not include all reported species. We thank the developers and curators of PubPlant for their efforts in collecting and maintaining the data. We thank W. J. Lucas, J. Zhang, Z. Liu and N. Wang for project discussions and critical comments. This project was funded by a Guangdong Major Project of Basic and Applied Basic Research (2021B0301030004), the National Natural Science Foundation of China (grant numbers 32488302 and 31991181), the Fundamental Research Fund for the Central Universities (77000-12240018), the Agricultural Science and Technology Innovation Program (CAAS-ZDRW202404) and a Shenzhen Outstanding Talents Training Fund. Z.B. is supported by the grants to D. Weigel.
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Q.Z., Z.B. and S.H. co-designed the framework of the paper. L.C., Z.B. and Q.Z. wrote the draft of the paper and generated the figures. Q.K., L.L., N.S. and S.H. contributed to writing and revision of the paper.
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Cheng, L., Bao, Z., Kong, Q. et al. Genome analyses and breeding of polyploid crops. Nat. Plants 11, 1714–1728 (2025). https://doi.org/10.1038/s41477-025-02088-5
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DOI: https://doi.org/10.1038/s41477-025-02088-5
