Genome analyses and breeding of polyploid crops

Lin Cheng^#^{1

2

3}, Zhigui Bao^#⁴, Qianqian Kong¹, Ludivine Lassois³, Nils Stein^{5

6}, Sanwen Huang^{2

7}, Qian Zhou^{8

9}

Affiliations

¹ School of Agriculture and Biotechnology, Sun Yat-Sen University, Shenzhen, China.
² National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
³ Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux, Belgium.
⁴ Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
⁵ Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
⁶ Crop Plant Genetics, Institute of Agricultural and Nutritional Sciences, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany.
⁷ National Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
⁸ School of Agriculture and Biotechnology, Sun Yat-Sen University, Shenzhen, China. zhouq289@mail.sysu.edu.cn.
⁹ Department of Network Intelligence, Peng Cheng Laboratory, Shenzhen, China. zhouq289@mail.sysu.edu.cn.

^# Contributed equally.

PMID: 40877448
DOI: 10.1038/s41477-025-02088-5

Review

Genome analyses and breeding of polyploid crops

Lin Cheng et al. Nat Plants. 2025.

. 2025 Aug 28.

doi: 10.1038/s41477-025-02088-5. Online ahead of print.

Authors

Lin Cheng^#^{1

2

3}, Zhigui Bao^#⁴, Qianqian Kong¹, Ludivine Lassois³, Nils Stein^{5

6}, Sanwen Huang^{2

7}, Qian Zhou^{8

9}

Affiliations

¹ School of Agriculture and Biotechnology, Sun Yat-Sen University, Shenzhen, China.
² National Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
³ Plant Genetics and Rhizosphere Processes Laboratory, TERRA Teaching and Research Center, University of Liège, Gembloux Agro-Bio Tech, Gembloux, Belgium.
⁴ Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
⁵ Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.
⁶ Crop Plant Genetics, Institute of Agricultural and Nutritional Sciences, Martin-Luther-University of Halle-Wittenberg, Halle (Saale), Germany.
⁷ National Key Laboratory of Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, China.
⁸ School of Agriculture and Biotechnology, Sun Yat-Sen University, Shenzhen, China. zhouq289@mail.sysu.edu.cn.
⁹ Department of Network Intelligence, Peng Cheng Laboratory, Shenzhen, China. zhouq289@mail.sysu.edu.cn.

^# Contributed equally.

PMID: 40877448
DOI: 10.1038/s41477-025-02088-5

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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Conflict of interest statement

Competing interests: The authors declare no competing interests.

References

1. Grant, V. Plant Speciation (Columbia Univ. Press, 1981).
1. Masterson, J. Stomatal size in fossil plants: evidence for polyploidy in majority of angiosperms. Science 264, 421–424 (1994). - PubMed
1. Cui, L. et al. Widespread genome duplications throughout the history of flowering plants. Genome Res. 16, 738–749 (2006). - PubMed - PMC
1. Dinesh Babu, K. S. et al. A short review on sugarcane: its domestication, molecular manipulations and future perspectives. Genet. Resour. Crop Evol. 69, 2623–2643 (2022). - PubMed - PMC
1. Healey, A. L. et al. The complex polyploid genome architecture of sugarcane. Nature 628, 804–810 (2024). - PubMed - PMC

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Genome analyses and breeding of polyploid crops

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Genome analyses and breeding of polyploid crops

Authors

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Conflict of interest statement

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