Abstract
Eggplant (Solanum melongena L.) is a globally important Solanaceae crop, yet trait-relevant genomic variants remain poorly characterized. Here, we perform population genomic analyses of 226 eggplant accessions sampled mainly from a major domestication center spanning Southeast Asia and South China, and find that genetic relationships closely track geographic origin. We generate chromosome-scale assemblies for 11 representative accessions using long-read sequencing and integrate six published genomes to build a pangenome resource. Using this resource, association scans identify a 12.4 Mb inversion on chromosome 10 segregating at 50.44% frequency that is strongly associated with fruit color, likely through hitchhiking with SmMYB1. We also detect variants associated with bacterial wilt resistance, including a premature stop codon in SmCYP82D47 and copy number variations in SmEPS1 and SmRoq1 homologs. Together, our results illuminate the evolution and phenotypic impact of large structural variants and provide genomic resources for eggplant genetics and breeding.
Data availability
All the raw sequencing data, genome assemblies and annotations have been submitted to China National GeneBank (CNGB) database under Project accession number CNP0006177. The variant (VCF) and pangenome graph files have been deposited in the Zenodo database [https://doi.org/10.5281/zenodo.18425195]. Source data are provided with this paper.
Code availability
The scripts associated with the pangenome analysis are available at Github (https://github.com/yiliao1022/eggplantpangenome) and Zendo (https://doi.org/10.5281/zenodo.18467477).
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Acknowledgements
We thank Y. Wang and C. Yu for help with the germplasm collection. This work was founded by grants from Guangdong S&T Program (Grant No. 2025B0202070003 to T.L.), the Guangdong Provincial Natural Science Foundation (Grant No. 2023A1515012563 and 2025A1515012414 to Q.Y.), the Guangdong Provincial Rural Revitalization Strategy Special Fund Seed Industry Revitalization Project (Grant No. 2022-NJS-00-005 and 2023-NJS-00-003 to Q.Y.), the Special fund for scientific innovation strategy-construction of high level Academy of Agriculture Science (Grant No. R2021YJ-YB3019 and R2023PY-QY004 to Q.Y.), Modern Seed Industry Innovation Capability Enhancement Project of Guangdong Academy of Agricultural Sciences (Grant No. 2025ZYTS0505 to T.L.), the Department of agriculture and rural areas of Guangdong province of China (Grant No. 2025-NBH-00-001 to B.S.), the Basic Research Project of Guangdong Vegetable Research Institute (Grant No. 202110 to Q.Y.), and Research Start-up Funding from South China Agricultural University to Y.L.
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Q.Y., Y.L., T.L., and B.S. conceived and designed the study. Z.L., T.L., and B.S. prepared the materials. Z.P., Y.L. and M.H. performed the pangenome and structural variation analyses. Q.Y., Y.J., P.W. and Y.Z. performed the GWAS analyses. W.Z., S.Z., H.C. and H.Z. contributed to the field phenotyping. Q.Y., W.Z., and S.Z. performed the gene silencing experiments. Y.L., Q.Y., Z.P., Z.L., Y.J., P.W., T.L., Y.Z., B.S., C.C., and B.S.G. wrote and revised the manuscript. All authors have read and approved the final manuscript.
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You, Q., Peng, Z., Li, Z. et al. Sub-pangenome analysis reveals structural variants associated with fruit color and bacterial wilt resistance in eggplant. Nat Commun (2026). https://doi.org/10.1038/s41467-026-69764-8
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DOI: https://doi.org/10.1038/s41467-026-69764-8
