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 multiple locations for agronomic, disease resistance and fruit metabolomic traits and resequenced. Forty chromosome-level assemblies of <i>S. melongena</i>, its progenitor <i>S. insanum</i> and the allied species <i>S. incanum</i> were generated to construct two graph-based pangenomes, which capture a broad spectrum of structural, nucleotide, and phenotypic variation, more than doubling the size of a previously published pangenome. Pangenome-wide association analyses were conducted, identifying a total of 3,192 marker-trait associations. We demonstrate the power of these analyses through examples such as the identification of major loci associated with the prickliness and resistance to <i>Fusarium oxysporum</i> f. sp. <i>melongenae</i>, driven by SVs affecting the <i>LONELY GUY</i> (<i>LOG</i>) 3 gene and a resistance gene clusters, respectively, as well as a mutation in a <i>GDSL-like esterase/lipase</i> gene altering the levels of isochlorogenic acids, important compounds linked to fruit browning and antioxidant properties. These datasets provide a solid basis for pangenome-assisted breeding in eggplant, and enable detailed analyses of genetic diversity, population demography, domestication history, and trait evolution.