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<p>Eggplant (<i>Solanum melongena</i> L.) is a major Solanaceous crop of Asian origin, but genomic resources remain limited compared to related species. Here, a core collection of 368 accessions spanning global diversity of <i>S. melongena</i> and wild relatives is phenotyped for agronomic, disease resistance and fruit metabolomic traits and resequenced. Additionally, 40 chromosome-level assemblies of <i>S. melongena</i>, its progenitor <i>S. insanum</i> and the allied species <i>S. incanum</i> enable the construction of two graph-based pangenomes, capturing broad genetic variation. We demonstrate the power of these datasets by identifying major loci controlling prickliness and resistance to <i>Fusarium oxysporum</i> f. sp. <i>melongenae</i>, driven by SVs affecting the <i>LONELY GUY 3</i> gene and a resistance gene cluster, respectively, as well as a mutation in a <i>GDSL-like esterase/lipase</i> gene altering the levels of dicaffeoyl-quinic acids. These findings provide a cornerstone for pangenome-assisted breeding, enabling detailed analyses of genetic diversity, domestication history, and trait evolution in eggplant.</p>

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Graph-based pangenomes and pan-phenome provide a cornerstone for eggplant biology and breeding

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年11月11日

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  • Luciana Gaccione,
  • Laura Toppino,
  • Marie Bolger,
  • Maximilian Schmidt,
  • Maria Rosaria Tassone,
  • Maria Sulli,
  • Emily Idahl,
  • David Alonso,
  • Giuseppe Aprea,
  • Paola Ferrante,
  • Véronique Lefebvre,
  • Hatice Filiz Boyaci,
  • Roland Schafleitner,
  • Stefano Gattolin,
  • Richard Finkers,
  • Matthijs Brouwer,
  • Arnaud Bovy,
  • Jaime Prohens,
  • Ezio Portis,
  • Sergio Lanteri,
  • Giuseppe Leonardo Rotino,
  • Giovanni Giuliano,
  • Björn Usadel,
  • Lorenzo Barchi

摘要

Eggplant (Solanum melongena L.) is a major Solanaceous crop of Asian origin, but genomic resources remain limited compared to related species. Here, a core collection of 368 accessions spanning global diversity of S. melongena and wild relatives is phenotyped for agronomic, disease resistance and fruit metabolomic traits and resequenced. Additionally, 40 chromosome-level assemblies of S. melongena, its progenitor S. insanum and the allied species S. incanum enable the construction of two graph-based pangenomes, capturing broad genetic variation. We demonstrate the power of these datasets by identifying major loci controlling prickliness and resistance to Fusarium oxysporum f. sp. melongenae, driven by SVs affecting the LONELY GUY 3 gene and a resistance gene cluster, respectively, as well as a mutation in a GDSL-like esterase/lipase gene altering the levels of dicaffeoyl-quinic acids. These findings provide a cornerstone for pangenome-assisted breeding, enabling detailed analyses of genetic diversity, domestication history, and trait evolution in eggplant.