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

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Pubblicato in:Nature Communications vol. 16, no. 1 (2025), p. 9919-9939
Autore principale: Gaccione, Luciana
Altri autori: Toppino, Laura, Bolger, Marie, Schmidt, Maximilian, Tassone, Maria Rosaria, Sulli, Maria, Idahl, Emily, Alonso, David, Aprea, Giuseppe, Ferrante, Paola, Lefebvre, Véronique, Boyaci, Hatice Filiz, Schafleitner, Roland, Gattolin, Stefano, Finkers, Richard, Brouwer, Matthijs, Bovy, Arnaud, Prohens, Jaime, Portis, Ezio, Lanteri, Sergio, Rotino, Giuseppe Leonardo, Giuliano, Giovanni, Usadel, Björn, Barchi, Lorenzo
Pubblicazione:
Nature Publishing Group
Soggetti:
Disease resistance
Genetic analysis
Phylogenetics
Evolution
Flowers & plants
Plant breeding
Domestication
Biosynthesis
Metabolomics
Chromosomes
Trees
Assemblies
Genomes
Genetic diversity
Genes
Association analysis
Fusarium oxysporum
Solanum melongena
Environmental
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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.Eggplants are important vegetables worldwide. Here, the authors report 40 genome assemblies of Solanum melongena, its progenitor S. insanum and the allied species S. incanum to construct two pangenomes, and identify loci associated with multiple traits via pangenome-wide association analysis.
ISSN:2041-1723
DOI:10.1038/s41467-025-64866-1
Fonte:Health & Medical Collection