Abstract
Heterosis arising from hybrid breeding has been instrumental in the improvement of crop yield and quality1,2. In self-pollinating crops, the use of male-sterile lines facilitates the production of hybrid seeds3. However, hybrid breeding in asexually propagated crops such as potato (Solanum tuberosum L.) presents challenges not only in hybrid seed production but also due to competition between above-ground (fruit) and below-ground (tuber) sinks. Here we developed self-incompatible homozygous diploid potatoes and hybrids through haploid breeding. This approach enables large-scale, low-cost hybrid seed production and eliminates aerial fruit formation, thereby avoiding sink competition between fruits and tubers and achieving a streamlined breeding design. Our strategy elevates the harvest index of hybrid potatoes, offering a paradigm for using heterosis and maximizing yield potential in asexually propagated crops.
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Data availability
The whole-genome sequencing and transcriptome data have been deposited at the National Center for Biotechnology Information under BioProject accession number PRJNA1250243. Source data are provided with this paper.
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Acknowledgements
This study was supported by the National Key Research and Development Program of China (grant no. 2021YFD1201400), the National Natural Science Foundation of China (grant nos 32525048, 32372695, 32302541, 32488302 and U2002204), the Agricultural Science and Technology Innovation Program (grant no. CAAS-ZDRW202404) and the China Postdoctoral Science Foundation (grant no. BX20230426).
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Contributions
C.Z. conceived the project and designed the study. X.J., P.W., X.H., D.L. and D.Q. conducted haploid induction, identification and chromosome doubling. D.L. performed the bioinformatics analysis. Y.L. conducted the karyotype analysis. D.L. and C.X. conducted the field trials. G.Z. provided the computing platform. D.L. wrote the draft manuscript. D.L., C.Z. and S.H. revised the draft to develop the final version of the manuscript.
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Nature Plants thanks Glenn Bryan 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 Genome-wide heterozygosity analysis and ploidy detection of YS1 and haploids.
a–c, Genome-wide distribution of SNP counts in YS1 (a), Haploid-1 (b) and Haploid-2 (c). The x-axis represents chromosomes, the y-axis indicates SNP counts. d–f, Flow cytometry analysis of YS1 (d), Haploid-1 (e) and Haploid-2 (f).
Extended Data Fig. 2 Genomic composition analysis of the two haploids.
The proportions of the genome contributed by A6-26 (blue) and E4-63 (red) are shown.
Extended Data Fig. 3 Flow cytometry analysis of ploidy levels.
The left two panels show diploid and tetraploid controls; the right two panels indicate DH-1 and tetraploid. The x-axis represents fluorescence intensity; the y-axis indicates cell counts.
Extended Data Fig. 4 Phenotypic characterization of haploids, doubled haploids and tetraploids.
All data were collected on per plant, the number of dots representing the number of individual plants. P-values are calculated by Student’s t-test (two-tailed). Data are presented as mean values +/– SD. n = 10 for haploid, doubled haploid and tetraploid in all panels.
Extended Data Fig. 5 Agarose gel electrophoresis verifies the successful cross between DM and DHs.
H1–H14 indicate different hybrid progeny plants. S3 is the S-RNase type in DM (a), while S4 is the S-RNase type in DH lines (b). Two repeats were conducted independently with similar results.
Extended Data Fig. 6 Yield and deleterious mutations analyses of diploid hybrids.
a, The upper and lower edges of the boxes denote 75% and 25% quartiles, and the central line indicates the median. Whiskers extend to the lower hinge –1.5× interquartile range and upper hinge +1.5× interquartile range of the data. The number of individual plants used for yield assessment is 68. b, Complementarity ratio of deleterious mutations in YS1, DM × DH-1 and DM × DH-2.
Extended Data Fig. 7 Pollen tube growth assays confirm self-incompatibility in DH-1 and DH-2.
Pollen tubes can reach ovules in YS1 (left panel), while they fail to reach ovules in DH-1 (middle panel) and DH-2 (right panel). Red arrowheads indicate the ends of pollen tubes. Two repeats were conducted independently with similar results.
Extended Data Fig. 8 Haploid-breeding workflow.
Detailed haploid-breeding workflow utilized by our group for one experienced breeding assistant working an 8-hour day. Within approximately 6–7 months, one breeding assistant can complete the entire process from crossing to haploid screening.
Supplementary information
Supplementary Table 1 (download XLSX )
The primers used in this study.
Supplementary Table 2 (download XLSX )
Statistical analysis of hybridization and haploid induction.
Source data
Source Data Fig. 1c (download JPG )
Unprocessed gels.
Source Data Fig. 2 and Extended Data Figs. 4 and 6 (download XLSX )
Statistical source data.
Source data Extended Data Fig. 5 (download JPG )
Unprocessed gels.
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Li, D., Jing, X., Wang, P. et al. Generating self-incompatible hybrid potatoes through haploid breeding. Nat. Plants 12, 496–502 (2026). https://doi.org/10.1038/s41477-026-02235-6
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DOI: https://doi.org/10.1038/s41477-026-02235-6
