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<p>Eggplant (<i>Solanum melongena</i> 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 <i>SmMYB1</i>. We also detect variants associated with bacterial wilt resistance, including a premature stop codon in <i>SmCYP82D47</i> and copy number variations in <i>SmEPS1</i> and <i>SmRoq1</i> homologs. Together, our results illuminate the evolution and phenotypic impact of large structural variants and provide genomic resources for eggplant genetics and breeding.</p>

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Sub-pangenome analysis reveals structural variants associated with fruit color and bacterial wilt resistance in eggplant

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年2月23日

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  • Qian You,
  • Ze Peng,
  • Zhiliang Li,
  • Yaolan Jiang,
  • Penglong Wan,
  • Yahui Zhao,
  • Wei Zhao,
  • Songyuan Zhang,
  • Hefen Cheng,
  • Chengjie Chen,
  • Zhou Heng,
  • Ming Hu,
  • Yongfeng Zhou,
  • Brandon S. Gaut,
  • Baojuan Sun,
  • Tao Li,
  • Yi Liao

摘要

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.