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Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon

Nature Genetics (2026)Cite this article

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Abstract

Pangenomes are increasingly important for harnessing crop genetic diversity, yet their resolution and utility are often limited by insufficient sampling of high-quality genome assemblies. Here we present a population-level watermelon super-pangenome constructed from 138 reference-grade assemblies, including 135 newly generated genomes representing all seven species. This super-pangenome captures approximately 1 million structural variants (SVs), enabling accurate variant genotyping across 914 accessions. Broader sampling within the pangenome provides insights into watermelon genome evolution and the origin of cultivated watermelon. Incorporating SVs into genome-wide association studies improves mapping resolution and reveals a copy number variant upstream of ClFCI1 that regulates flesh color intensity in a dosage-dependent manner. Leveraging this comprehensive variation map, we developed high-accuracy genomic prediction models for 18 agronomic traits. Together, these findings and genomic resources establish a foundation for dissecting complex traits and accelerating precision breeding in watermelon, while offering a valuable model for SV-resolved pangenomics in crops.

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Fig. 1: Genome evolution in the Citrullus genus.
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Fig. 2: Gene pool dynamics in the Citrullus genus.
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Fig. 3: Landscape of structural variation across Citrullus species.
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Fig. 4: Copy number variation in the promoter region of ClFCI1 controls watermelon flesh color intensity.
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Fig. 5: Graph-based pangenome empowers genomic selection in watermelon.
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Data availability

Raw HiFi, ONT, Hi–C and genome resequencing reads, as well as genome assemblies, have been deposited in the NCBI BioProject database under accession PRJNA1272048. Individual accession numbers for genome assemblies and raw sequencing datasets are provided in Supplementary Tables 1 and 10. Genome assemblies and annotations, and variant files in VCF format are available at CuGenDBv2 (http://cucurbitgenomics.org/v2/ftp/pan-genome/watermelon/graph_pangenome/).

Code availability

No custom code was generated in this study. All software used in this study is publicly or commercially available as described in the Methods and Reporting Summary.

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Acknowledgements

The authors thank S.S. Renner from University of Munich for providing seeds of C. lanatus subsp. cordophanus. This research was supported by the Beijing Rural Revitalization Agricultural Science and Technology Project (grant NY2401130025 to Y.X.), the National Natural Science Foundation of China (grants 32172592 to J. Zhang and 32330093 to Y.X.), the Scientific and Technological Innovation Capacity Building Project of BAAFS (KJCX20251008 to J. Zhang), the Scientist Training Program of BAAFS (JKZX202401 to J. Zhang), Ministry of Agriculture of China (CARS-25 to Y.X.) and USDA National Institute of Food and Agriculture Specialty Crop Research Initiative (2015-51181-24285 and 2020-51181-32139 to Z.F., R.G., A.L., C.K., S.E.B., P.W. and C.M.).

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Author notes

  1. These authors contributed equally: Honghe Sun, Jie Zhang, Shengjin Liao, Shaogui Guo, Zhe Zhou.

Authors and Affiliations

  1. Boyce Thompson Institute, Cornell University, Ithaca, NY, USA

    Honghe Sun, Zhe Zhou, Xuebo Zhao, Shan Wu, Jiantao Zhao & Zhangjun Fei

  2. State Key Laboratory of Vegetable Biobreeding, National Engineering Research Center for Vegetables, Beijing Key Laboratory of Crop Molecular Design and Intelligent Breeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China

    Honghe Sun, Jie Zhang, Shengjin Liao, Shaogui Guo, Guoyi Gong, Jinfang Wang, Maoying Li, Yongtao Yu, Yi Ren, Shouwei Tian, Shaofang Li, Haiying Zhang & Yong Xu

  3. Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA

    Honghe Sun

  4. Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China

    Zhe Zhou

  5. Department of Horticulture, Graduate Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI, USA

    Sue A. Hammar & Rebecca Grumet

  6. Department of Horticulture, University of Georgia, Athens, GA, USA

    Cecilia McGregor

  7. U.S. Department of Agriculture-Agricultural Research Service, Plant Genetic Resources Conservation Unit, Griffin, GA, USA

    Robert Jarret

  8. Coastal Research and Education Center, Clemson University, Charleston, SC, USA

    Patrick Wechter & Sandra E. Branham

  9. U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Lab, Charleston, SC, USA

    Chandrasekar Kousik & Amnon Levi

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Contributions

Z.F. and Y.X. designed and supervised the project. S.G., S.A.H., C.M., R.J., S.E.B., P.W., C.K., A.L. and R.G. contributed to sample collection and DNA extraction. S.G., H.S., S. Liao, J. Zhang, R.J. and Z.F. coordinated genome sequencing. S.G., S. Liao, J. Zhang, G.G., J.W., M.L., Y.Y., Y.R., S.T., S. Li and H.Z. performed phenotyping for fruit-quality traits. H.S., Z.Z., X.Z. and S.W. contributed to genome assembly and annotation, as well as pangenome and population genetic analyses. H.S. and J. Zhao conducted the genomic prediction analysis. J. Zhang, H.S. and S. Liao contributed to genetic mapping and gene functional characterization. H.S., Z.Z., J. Zhang, X.Z. and S.W. wrote the manuscript. Z.F. and Y.X. revised the manuscript.

Corresponding authors

Correspondence to Zhangjun Fei or Yong Xu.

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All authors declare no competing interests.

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Nature Genetics thanks Michael Bevan, Hongbo Li, and the other anonymous reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available.

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Extended data

Extended Data Fig. 1 Closely located large inversions on chromosome 6 encompassing QTLs associated with Fusarium wilt resistance, flesh sweetness and flesh firmness.

a, A genomic region on chromosome 6 (green box) in cultivated watermelon introgressed from C. amarus, overlapping with three QTLs related to Fusarium wilt resistance (qFon2-6), flesh sweetness (QBrix6), and flesh firmness. b, Alignments of chromosome 6 between reference ‘97103’ and the accessions ‘SugarleeXZ’, ‘PI 264341-FR’, and ‘USVL252’, all of which harbor resistance to Fusarium wilt.

Extended Data Fig. 2 Haplotypes of the fruit shape-related gene ClFS1.

a, Structure diagram of the missense SNP (ClFS1Hap2) and 159-bp deletion (ClFS1Hap3) in ClFS1. Representative fruits carrying the corresponding haplotypes are shown. ClFS1Hap1 denotes the reference allele from ‘97103’. FSI, fruit shape index. Scale bars, 10 cm. b, Allele frequencies of the three haplotypes across Citrullus groups. c, Effect of different haplotypes of ClFS1 on fruit shape. In c, P values were calculated using two-sided Student’s t-test.

Extended Data Fig. 3 Genetic mapping of flesh color intensity in watermelon.

a, Genome-wide ΔSNP-index profile from bulked-segregant analysis (BSA) of an F2 population derived from the cross ‘Ming 58’ (scarlet flesh) x ‘JX2’ (pink flesh). The black curve represents ΔSNP-index values, while red and blue envelopes mark the 95% and 99% confidence thresholds, respectively. b,c, Recombinant-based fine-mapping of the ClFCI1 locus in 141 F2 plants from the ‘Ming 58’ x ‘JX2’ cross (b), and 636 F2 plants from the ‘JLM’ x ‘Cream of Saskatchewan’ (CS) cross (c). Top, fruits of parental lines and F1 hybrids. Scale bars, 10 cm. Middle, QTL curves showing logarithm of odds (LOD) scores using KASP markers between 23 Mb and 26 Mb on chromosome 6. Bottom, graphical genotypes of key recombinant individuals. Pink, red, and scarlet segments denote homozygous ‘JX2’, heterozygous, and homozygous ‘Ming 58’ regions, respectively; pale yellow, orange, and yellow segments denote homozygous ‘CS’, heterozygous, and homozygous ‘JLM’ regions, respectively. d, Relative expression levels of candidate genes in the four parental lines (‘Ming 58’, ‘JX2’, ‘JLM’, and ‘CS’). Error bars indicate the standard deviation of three biological replicates. Different lowercase letters indicate significant differences according to Turkey’s multiple range test (P < 0.05).

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Sun, H., Zhang, J., Liao, S. et al. Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon. Nat Genet (2026). https://doi.org/10.1038/s41588-026-02598-8

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