Graph-based pangenomes and pan-phenome provide a cornerstone for eggplant biology and breeding
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.
Authors
- Arnaud Bovy (ORCID: https://orcid.org/0000-0003-2643-7377)
- Giuseppe Aprea (ORCID: https://orcid.org/0000-0003-4969-2696)
- Lorenzo Barchi (ORCID: https://orcid.org/0000-0001-6414-4239)
- Björn Usadel (ORCID: https://orcid.org/0000-0003-0921-8041)
- Giuseppe Leonardo Rotino (ORCID: https://orcid.org/0000-0001-9138-0958)
- Luciana Gaccione (ORCID: https://orcid.org/0000-0001-5194-0754)
- Giovanni Giuliano (ORCID: https://orcid.org/0000-0002-2486-0510)
- Maximilian Schmidt (ORCID: https://orcid.org/0000-0001-8710-1389)
- Maria Rosaria Tassone (ORCID: https://orcid.org/0009-0003-3213-3078)
- Laura Toppino (ORCID: https://orcid.org/0000-0002-8664-1233)
- Stefano Gattolin (ORCID: https://orcid.org/0000-0003-3855-9160)
- Paola Ferrante (ORCID: https://orcid.org/0000-0003-3071-2212)
- David Alonso (ORCID: https://orcid.org/0000-0002-4598-9719)
- Sergio Lanteri (ORCID: https://orcid.org/0000-0003-3012-8710)
- Roland Schafleitner (ORCID: https://orcid.org/0000-0003-3637-7603)
- Matthijs Brouwer (ORCID: https://orcid.org/0000-0001-8183-0484)
- Hatice Filiz Boyacı (ORCID: https://orcid.org/0000-0002-3799-4673)
- Ezio Portis (ORCID: https://orcid.org/0000-0002-1548-6096)
- Véronique Lefèbvre (ORCID: https://orcid.org/0000-0001-9916-8433)
- Maria Sulli (ORCID: https://orcid.org/0000-0002-6875-2546)
- Marie Bolger (ORCID: https://orcid.org/0000-0001-6335-1578)
- Richard Finkers (ORCID: https://orcid.org/0000-0002-4368-8058)
- Emily Idahl
Institutions
- National Agency for New Technologies, Energy and Sustainable Economic Development (IT)
- World Vegetable Center (TW)
- Centro Studi GISED (IT)
- Recep Tayyip Erdoğan University (TR)
- Forschungszentrum Jülich (DE)
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement (FR)
- Graduate School Experimental Plant Sciences (NL)
- Institute of Agricultural Biology and Biotechnology (IT)
- Associazione Regionale Allevatori della Lombardia (IT)
- Génétique et amélioration des fruits et légumes (FR)
- Hochschule Geisenheim University (DE)
- Heinrich Heine University Düsseldorf (DE)
- University of Turin (IT)
- Universitat Politècnica de València (ES)
- Wageningen University & Research (NL)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-11-11
- DOI
- https://doi.org/10.1038/s41467-025-64866-1
- Citations
- 6
- Primary Topic
- Plant Pathogens and Fungal Diseases
- Type
- article
- Field-Weighted Citation Impact
- 6.91
Funders
- European Commission
- HORIZON EUROPE Framework Programme