Graph-based pangenomes and pan-phenome provide a cornerstone for eggplant biology and breeding
A core collection of 368 accessions representing the worldwide diversity of <i>Solanum melongena</i> and several wild relatives was phenotyped in multiple locations for agronomic, disease resistance and fruit metabolomic traits and resequenced. Additionally, forty chromosome-level assemblies of <i>S. melongena</i>, its progenitor <i>S. insanum</i> and the allied species <i>S. incanum</i> allowed the construction of two graph-based pangenomes, capturing a broad spectrum of genetic variation in the core collection. Here, we demonstrate the power of these datasets by identifying major loci associated with 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, and enable detailed analyses of genetic diversity, domestication history, and trait evolution in eggplant.