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

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 () and Lorenzo Barchi ()
Additional contact information
Luciana Gaccione: University of Turin
Laura Toppino: Research Centre for Genomics and Bioinformatics
Marie Bolger: Forschungzentrum Jülich
Maximilian Schmidt: Geisenheim University
Maria Rosaria Tassone: Research Centre for Genomics and Bioinformatics
Maria Sulli: Casaccia Res Ctr
Emily Idahl: Heinrich Heine University
David Alonso: Universitat Politècnica de València
Giuseppe Aprea: Casaccia Res Ctr
Paola Ferrante: Casaccia Res Ctr
Véronique Lefebvre: GAFL
Hatice Filiz Boyaci: University of Recep Tayyip Erdogan
Roland Schafleitner: The World Vegetable Center
Stefano Gattolin: Institute of Agricultural Biology and Biotechnology (IBBA-CNR)
Richard Finkers: Wageningen University & Research WUR
Matthijs Brouwer: Wageningen University & Research WUR
Arnaud Bovy: Wageningen University & Research WUR
Jaime Prohens: Universitat Politècnica de València
Ezio Portis: University of Turin
Sergio Lanteri: University of Turin
Giuseppe Leonardo Rotino: Research Centre for Genomics and Bioinformatics
Giovanni Giuliano: Casaccia Res Ctr
Björn Usadel: Forschungzentrum Jülich
Lorenzo Barchi: University of Turin

Nature Communications, 2025, vol. 16, issue 1, 1-20

Abstract: Abstract 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.

Date: 2025
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DOI: 10.1038/s41467-025-64866-1

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